diff --git a/conf/test.config b/conf/test.config
index c7635451..3b306c17 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -24,21 +24,22 @@ params {
// Input data
// TODO params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
- input = "${projectDir}/assets/samplesheet.csv"
+ input = "${projectDir}/assets/samplesheet.csv"
// Genome references
- fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/GRCh38_chr21.fa'
- gtf = 'https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/genes_chr21.gtf'
- hisat2_index = 'https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/GRCh38_chr21_hisat2.tar.gz'
+ fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/GRCh38_chr21.fa'
+ gtf = 'https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/genes_chr21.gtf'
+ hisat2_index = 'https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/GRCh38_chr21_hisat2.tar.gz'
- assay_type = "GROseq"
- skip_grohmm = true // FIXME Fails due to higher memory requirements
+ assay_type = "GROseq"
+ // FIXME Fails due to higher memory requirements
+ skip_grohmm = true
grohmm_min_uts = 5
grohmm_max_uts = 10
grohmm_min_ltprobb = -100
grohmm_max_ltprobb = -150
- filter_bed = "${projectDir}/tests/config/unwanted_region.bed"
- intersect_bed = "${projectDir}/tests/config/wanted_region.bed"
+ filter_bed = "${projectDir}/tests/config/unwanted_region.bed"
+ intersect_bed = "${projectDir}/tests/config/wanted_region.bed"
}
process {
@@ -46,8 +47,7 @@ process {
ext.args = '--genomeSAindexNbases 9'
}
- withName: 'PINTS_CALLER' {
- // HACK Tests fail after latest modules update
+ withName: PINTS_CALLER {
ext.args = { "--disable-small" }
}
}
diff --git a/conf/test_copro.config b/conf/test_copro.config
index 27d33607..42c41cdd 100644
--- a/conf/test_copro.config
+++ b/conf/test_copro.config
@@ -15,17 +15,17 @@ params {
config_profile_description = 'Test dataset to check PINTS pipeline function(https://pints.yulab.org/tre_calling#part-iv-case-2)'
// Input data
- input = "${projectDir}/tests/config/samplesheets/copro.csv"
+ input = "${projectDir}/tests/config/samplesheets/copro.csv"
- genome = 'hg38'
- assay_type = 'CoPRO'
- filter_bed = "https://pints.yulab.org/ref/examples/promoters_1kb_tss_centered.bed.gz"
- with_umi = true
- umitools_dedup_stats = true
+ genome = 'hg38'
+ assay_type = 'CoPRO'
+ filter_bed = "https://pints.yulab.org/ref/examples/promoters_1kb_tss_centered.bed.gz"
+ with_umi = true
+ umitools_dedup_stats = true
}
process {
- withName: NFCORE_NASCENT:NASCENT:FASTP {
+ withName: FASTP {
ext.args = [
"--adapter_sequence TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC",
"--adapter_sequence_r2 GATCGTCGGACTGTAGAACTCTGAAC",
diff --git a/conf/test_full.config b/conf/test_full.config
index f5f1c5e6..5b464fe2 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -16,9 +16,9 @@ params {
// Input data for full size test
// TODO params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
- input = "${projectDir}/assets/samplesheet_full.csv"
+ input = "${projectDir}/assets/samplesheet_full.csv"
// Genome references
- genome = 'hg38'
- assay_type = 'GROseq'
+ genome = 'hg38'
+ assay_type = 'GROseq'
}
diff --git a/conf/test_grocap.config b/conf/test_grocap.config
index 53916d5f..55a1823b 100644
--- a/conf/test_grocap.config
+++ b/conf/test_grocap.config
@@ -15,21 +15,22 @@ params {
config_profile_description = 'Test dataset to check PINTS pipeline function(https://pints.yulab.org/tre_calling#part-iii-case-1)'
// Input data
- input = "${projectDir}/tests/config/samplesheets/grocap.csv"
+ input = "${projectDir}/tests/config/samplesheets/grocap.csv"
- genome = 'hg38'
- assay_type = 'GROcap'
- filter_bed = "https://pints.yulab.org/ref/examples/promoters_1kb_tss_centered.bed.gz"
+ genome = 'hg38'
+ assay_type = 'GROcap'
+ filter_bed = "https://pints.yulab.org/ref/examples/promoters_1kb_tss_centered.bed.gz"
}
process {
- withName: NFCORE_NASCENT:NASCENT:FASTP {
+ // only keep reads longer than 14nts after trimming
+ // This library was polyadenylated,
+ // so we are trimming the last 20nts per reads (with --trim_tail1).
+ // For more recent single-end PRO/GRO-cap libraries, this may not be necessary.
+ withName: 'NFCORE_NASCENT:NASCENT:FASTP' {
ext.args = [
"--adapter_sequence TGGAATTCTCGGGTGCCAAGG",
- "-l 14", // only keep reads longer than 14nts after trimming
- // This library was polyadenylated,
- // so we are trimming the last 20nts per reads (with --trim_tail1).
- // For more recent single-end PRO/GRO-cap libraries, this may not be necessary.
+ "-l 14",
"--trim_tail1 20",
"--low_complexity_filter",
"-w 8"
diff --git a/modules/local/bed2saf.nf b/modules/local/bed2saf.nf
index f23b7750..bcc23c3e 100644
--- a/modules/local/bed2saf.nf
+++ b/modules/local/bed2saf.nf
@@ -1,11 +1,11 @@
process BED2SAF {
- tag "$meta.id"
+ tag "${meta.id}"
label 'process_single'
conda "conda-forge::gawk=5.1.0"
- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
- 'nf-core/ubuntu:20.04' }"
+ container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+ ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04'
+ : 'nf-core/ubuntu:20.04'}"
input:
tuple val(meta), path(bed)
@@ -20,7 +20,7 @@ process BED2SAF {
script:
"""
awk 'OFS="\\t" {print \$1"."\$2"."\$3, \$1, \$2, \$3, "."}' \\
- $bed \\
+ ${bed} \\
> ${bed.baseName}.saf
cat <<-END_VERSIONS > versions.yml
diff --git a/modules/local/dreg_prep/main.nf b/modules/local/dreg_prep/main.nf
index 7c640cf4..403bdfdb 100644
--- a/modules/local/dreg_prep/main.nf
+++ b/modules/local/dreg_prep/main.nf
@@ -1,16 +1,16 @@
process DREG_PREP {
- tag "$meta.id"
+ tag "${meta.id}"
label 'process_low'
conda "${moduleDir}/environment.yml"
- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/mulled-v2-f01e242bdea19948f0576fdca94777242fe4c2cb:4238fb992d2a93e648108c86e3a9f51348e834a9-0' :
- 'biocontainers/mulled-v2-f01e242bdea19948f0576fdca94777242fe4c2cb:4238fb992d2a93e648108c86e3a9f51348e834a9-0' }"
+ container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+ ? 'https://depot.galaxyproject.org/singularity/mulled-v2-f01e242bdea19948f0576fdca94777242fe4c2cb:4238fb992d2a93e648108c86e3a9f51348e834a9-0'
+ : 'biocontainers/mulled-v2-f01e242bdea19948f0576fdca94777242fe4c2cb:4238fb992d2a93e648108c86e3a9f51348e834a9-0'}"
input:
tuple val(meta), path(bam_file), val(index)
- path sizes
+ path sizes
val assay_type
output:
@@ -78,10 +78,11 @@ process DREG_PREP {
echo "bedGraph to bigwig done"
"""
- } else {
+ }
+ else {
if (forwardStranded) {
"""
- samtools view -@ $task.cpus -bf 0x2 ${bam_file} | samtools sort -n -@ $task.cpus \\
+ samtools view -@ ${task.cpus} -bf 0x2 ${bam_file} | samtools sort -n -@ ${task.cpus} \\
> ${prefix}.dreg.bam
bedtools bamtobed -bedpe -mate1 -i ${prefix}.dreg.bam \\
@@ -118,9 +119,10 @@ process DREG_PREP {
${prefix}.unsorted.bedGraph \\
> ${prefix}.bedGraph
"""
- } else {
+ }
+ else {
"""
- samtools view -@ $task.cpus -bf 0x2 ${bam_file} | samtools sort -n -@ $task.cpus \\
+ samtools view -@ ${task.cpus} -bf 0x2 ${bam_file} | samtools sort -n -@ ${task.cpus} \\
> ${prefix}.dreg.bam
bedtools bamtobed -bedpe -mate1 -i ${prefix}.dreg.bam \\
diff --git a/modules/local/grohmm/parametertuning/main.nf b/modules/local/grohmm/parametertuning/main.nf
index ac56402f..b19810ce 100644
--- a/modules/local/grohmm/parametertuning/main.nf
+++ b/modules/local/grohmm/parametertuning/main.nf
@@ -1,12 +1,12 @@
process GROHMM_PARAMETERTUNING {
- tag "$meta.id|$UTS|$LtProbB"
+ tag "${meta.id}|${UTS}|${LtProbB}"
label 'process_high'
// array 10
conda "${moduleDir}/environment.yml"
- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b929af5662486ba6ce2d27eb501e5c7ec71ca7dd8e333fe5d3dcf2803d87cf67/data' :
- 'community.wave.seqera.io/library/grohmm:833aa94cad4202ac' }"
+ container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+ ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b929af5662486ba6ce2d27eb501e5c7ec71ca7dd8e333fe5d3dcf2803d87cf67/data'
+ : 'community.wave.seqera.io/library/grohmm:833aa94cad4202ac'}"
input:
tuple val(meta), path(bams), path(bais), val(UTS), val(LtProbB)
@@ -15,7 +15,7 @@ process GROHMM_PARAMETERTUNING {
output:
tuple val(meta), path("*.tuning.csv"), emit: tuning
tuple val(meta), path("*.tuning.consensus.bed"), emit: bed
- path "versions.yml", emit: versions
+ path "versions.yml", emit: versions
when:
task.ext.when == null || task.ext.when
@@ -27,12 +27,12 @@ process GROHMM_PARAMETERTUNING {
grohmm_parametertuning.R \\
--bam_file ${bams} \\
--outprefix ${prefix} \\
- --gxf $gxf \\
- --uts $UTS \\
- --ltprobb $LtProbB \\
+ --gxf ${gxf} \\
+ --uts ${UTS} \\
+ --ltprobb ${LtProbB} \\
--outdir ./ \\
- --cores $task.cpus \\
- $args
+ --cores ${task.cpus} \\
+ ${args}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
diff --git a/modules/local/grohmm/transcriptcalling/main.nf b/modules/local/grohmm/transcriptcalling/main.nf
index 984d1800..95dca60c 100644
--- a/modules/local/grohmm/transcriptcalling/main.nf
+++ b/modules/local/grohmm/transcriptcalling/main.nf
@@ -1,12 +1,12 @@
process GROHMM_TRANSCRIPTCALLING {
- tag "$meta.id"
+ tag "${meta.id}"
label 'process_high'
label 'process_long'
conda "${moduleDir}/environment.yml"
- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b929af5662486ba6ce2d27eb501e5c7ec71ca7dd8e333fe5d3dcf2803d87cf67/data' :
- 'community.wave.seqera.io/library/grohmm:833aa94cad4202ac' }"
+ container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+ ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b929af5662486ba6ce2d27eb501e5c7ec71ca7dd8e333fe5d3dcf2803d87cf67/data'
+ : 'community.wave.seqera.io/library/grohmm:833aa94cad4202ac'}"
input:
tuple val(meta), path(bams), path(bais), path(tuning_file)
@@ -14,12 +14,12 @@ process GROHMM_TRANSCRIPTCALLING {
output:
tuple val(meta), path("*.transcripts.txt"), emit: transcripts
- tuple val(meta), path("*.eval.txt") , emit: eval
+ tuple val(meta), path("*.eval.txt"), emit: eval
tuple val(meta), path("*.transcripts.bed"), emit: transcripts_bed
- tuple val(meta), path("*.tdFinal.txt") , emit: td
- tuple val(meta), path("*.tdplot_mqc.png") , emit: td_plot
- tuple val(meta), path("*.tdFinal_mqc.csv") , emit: mqc_csv
- path "versions.yml" , emit: versions
+ tuple val(meta), path("*.tdFinal.txt"), emit: td
+ tuple val(meta), path("*.tdplot_mqc.png"), emit: td_plot
+ tuple val(meta), path("*.tdFinal_mqc.csv"), emit: mqc_csv
+ path "versions.yml", emit: versions
when:
task.ext.when == null || task.ext.when
@@ -32,11 +32,11 @@ process GROHMM_TRANSCRIPTCALLING {
--bam_file ${bams} \\
--tuning_file ${tuning_file} \\
--outprefix ${prefix} \\
- --gxf $gxf \\
+ --gxf ${gxf} \\
--outdir ./ \\
- --cores $task.cpus \\
+ --cores ${task.cpus} \\
--memory ${task.memory.toMega()} \\
- $args
+ ${args}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
diff --git a/modules/local/gtf2bed.nf b/modules/local/gtf2bed.nf
index 07df95fb..7b34be8b 100644
--- a/modules/local/gtf2bed.nf
+++ b/modules/local/gtf2bed.nf
@@ -1,26 +1,27 @@
process GTF2BED {
- tag "$gtf"
+ tag "${gtf}"
label 'process_low'
conda "conda-forge::perl=5.26.2"
- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/perl:5.26.2' :
- 'biocontainers/perl:5.26.2' }"
+ container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+ ? 'https://depot.galaxyproject.org/singularity/perl:5.26.2'
+ : 'biocontainers/perl:5.26.2'}"
input:
path gtf
output:
- path '*.bed' , emit: bed
+ path '*.bed', emit: bed
path "versions.yml", emit: versions
when:
task.ext.when == null || task.ext.when
- script: // This script is bundled with the pipeline, in nf-core/nascent/bin/
+ script:
+ // This script is bundled with the pipeline, in nf-core/nascent/bin/
"""
gtf2bed \\
- $gtf \\
+ ${gtf} \\
> ${gtf.baseName}.bed
cat <<-END_VERSIONS > versions.yml
diff --git a/subworkflows/local/align_bwamem2/main.nf b/subworkflows/local/align_bwamem2/main.nf
index beb6d863..f1ffb959 100644
--- a/subworkflows/local/align_bwamem2/main.nf
+++ b/subworkflows/local/align_bwamem2/main.nf
@@ -2,15 +2,15 @@
// Alignment with BWAMEM2
//
-include { BWAMEM2_MEM } from '../../../modules/nf-core/bwamem2/mem/main'
+include { BWAMEM2_MEM } from '../../../modules/nf-core/bwamem2/mem/main'
include { BAM_SORT_STATS_SAMTOOLS } from '../../nf-core/bam_sort_stats_samtools/main'
workflow ALIGN_BWAMEM2 {
take:
- ch_reads // channel (mandatory): [ val(meta), [ path(reads) ] ]
- ch_index // channel (mandatory): [ val(meta2), path(index) ]
- val_sort_bam // boolean (mandatory): true or false
- ch_fasta // channel (optional) : [ val(meta3), path(fasta) ]
+ ch_reads // channel (mandatory): [ val(meta), [ path(reads) ] ]
+ ch_index // channel (mandatory): [ val(meta2), path(index) ]
+ val_sort_bam // boolean (mandatory): true or false
+ ch_fasta // channel (optional) : [ val(meta3), path(fasta) ]
main:
ch_versions = Channel.empty()
@@ -19,25 +19,23 @@ workflow ALIGN_BWAMEM2 {
// Map reads with BWA
//
- BWAMEM2_MEM ( ch_reads, ch_index, ch_fasta, val_sort_bam )
+ BWAMEM2_MEM(ch_reads, ch_index, ch_fasta, val_sort_bam)
ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
//
// Sort, index BAM file and run samtools stats, flagstat and idxstats
//
- BAM_SORT_STATS_SAMTOOLS ( BWAMEM2_MEM.out.bam, ch_fasta )
+ BAM_SORT_STATS_SAMTOOLS(BWAMEM2_MEM.out.bam, ch_fasta)
ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS.out.versions)
emit:
- bam_orig = BWAMEM2_MEM.out.bam // channel: [ val(meta), path(bam) ]
-
- bam = BAM_SORT_STATS_SAMTOOLS.out.bam // channel: [ val(meta), path(bam) ]
- bai = BAM_SORT_STATS_SAMTOOLS.out.bai // channel: [ val(meta), path(bai) ]
- csi = BAM_SORT_STATS_SAMTOOLS.out.csi // channel: [ val(meta), path(csi) ]
- stats = BAM_SORT_STATS_SAMTOOLS.out.stats // channel: [ val(meta), path(stats) ]
+ bam_orig = BWAMEM2_MEM.out.bam // channel: [ val(meta), path(bam) ]
+ bam = BAM_SORT_STATS_SAMTOOLS.out.bam // channel: [ val(meta), path(bam) ]
+ bai = BAM_SORT_STATS_SAMTOOLS.out.bai // channel: [ val(meta), path(bai) ]
+ csi = BAM_SORT_STATS_SAMTOOLS.out.csi // channel: [ val(meta), path(csi) ]
+ stats = BAM_SORT_STATS_SAMTOOLS.out.stats // channel: [ val(meta), path(stats) ]
flagstat = BAM_SORT_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), path(flagstat) ]
idxstats = BAM_SORT_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), path(idxstats) ]
-
- versions = ch_versions // channel: [ path(versions.yml) ]
+ versions = ch_versions // channel: [ path(versions.yml) ]
}
diff --git a/subworkflows/local/align_dragmap/main.nf b/subworkflows/local/align_dragmap/main.nf
index 17a74ec6..73a181b8 100644
--- a/subworkflows/local/align_dragmap/main.nf
+++ b/subworkflows/local/align_dragmap/main.nf
@@ -2,15 +2,15 @@
// Alignment with dragmap
//
-include { DRAGMAP_ALIGN } from '../../../modules/nf-core/dragmap/align/main'
+include { DRAGMAP_ALIGN } from '../../../modules/nf-core/dragmap/align/main'
include { BAM_SORT_STATS_SAMTOOLS } from '../../nf-core/bam_sort_stats_samtools/main'
workflow ALIGN_DRAGMAP {
take:
- ch_reads // channel (mandatory): [ val(meta), [ path(reads) ] ]
- ch_index // channel (mandatory): [ val(meta2), path(index) ]
- val_sort_bam // boolean (mandatory): true or false
- ch_fasta // channel (optional) : [ val(meta3), path(fasta) ]
+ ch_reads // channel (mandatory): [ val(meta), [ path(reads) ] ]
+ ch_index // channel (mandatory): [ val(meta2), path(index) ]
+ val_sort_bam // boolean (mandatory): true or false
+ ch_fasta // channel (optional) : [ val(meta3), path(fasta) ]
main:
ch_versions = Channel.empty()
@@ -19,25 +19,23 @@ workflow ALIGN_DRAGMAP {
// Map reads with dragmap
//
- DRAGMAP_ALIGN ( ch_reads, ch_index, ch_fasta, val_sort_bam )
+ DRAGMAP_ALIGN(ch_reads, ch_index, ch_fasta, val_sort_bam)
ch_versions = ch_versions.mix(DRAGMAP_ALIGN.out.versions.first())
//
// Sort, index BAM file and run samtools stats, flagstat and idxstats
//
- BAM_SORT_STATS_SAMTOOLS ( DRAGMAP_ALIGN.out.bam, ch_fasta )
+ BAM_SORT_STATS_SAMTOOLS(DRAGMAP_ALIGN.out.bam, ch_fasta)
ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS.out.versions)
emit:
- bam_orig = DRAGMAP_ALIGN.out.bam // channel: [ val(meta), path(bam) ]
-
- bam = BAM_SORT_STATS_SAMTOOLS.out.bam // channel: [ val(meta), path(bam) ]
- bai = BAM_SORT_STATS_SAMTOOLS.out.bai // channel: [ val(meta), path(bai) ]
- csi = BAM_SORT_STATS_SAMTOOLS.out.csi // channel: [ val(meta), path(csi) ]
- stats = BAM_SORT_STATS_SAMTOOLS.out.stats // channel: [ val(meta), path(stats) ]
+ bam_orig = DRAGMAP_ALIGN.out.bam // channel: [ val(meta), path(bam) ]
+ bam = BAM_SORT_STATS_SAMTOOLS.out.bam // channel: [ val(meta), path(bam) ]
+ bai = BAM_SORT_STATS_SAMTOOLS.out.bai // channel: [ val(meta), path(bai) ]
+ csi = BAM_SORT_STATS_SAMTOOLS.out.csi // channel: [ val(meta), path(csi) ]
+ stats = BAM_SORT_STATS_SAMTOOLS.out.stats // channel: [ val(meta), path(stats) ]
flagstat = BAM_SORT_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), path(flagstat) ]
idxstats = BAM_SORT_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), path(idxstats) ]
-
- versions = ch_versions // channel: [ path(versions.yml) ]
+ versions = ch_versions // channel: [ path(versions.yml) ]
}
diff --git a/subworkflows/local/coverage_graphs.nf b/subworkflows/local/coverage_graphs.nf
index a1628c16..ac8c46db 100644
--- a/subworkflows/local/coverage_graphs.nf
+++ b/subworkflows/local/coverage_graphs.nf
@@ -2,15 +2,13 @@
* Create bigWig and bedGraph files
*/
-include {
- BEDTOOLS_GENOMECOV as BEDTOOLS_GENOMECOV_PLUS
- BEDTOOLS_GENOMECOV as BEDTOOLS_GENOMECOV_MINUS } from '../../modules/nf-core/bedtools/genomecov/main'
+include { BEDTOOLS_GENOMECOV as BEDTOOLS_GENOMECOV_PLUS } from '../../modules/nf-core/bedtools/genomecov/main'
+include { BEDTOOLS_GENOMECOV as BEDTOOLS_GENOMECOV_MINUS } from '../../modules/nf-core/bedtools/genomecov/main'
-include {
- DEEPTOOLS_BAMCOVERAGE as DEEPTOOLS_BAMCOVERAGE_PLUS
- DEEPTOOLS_BAMCOVERAGE as DEEPTOOLS_BAMCOVERAGE_MINUS } from '../../modules/nf-core/deeptools/bamcoverage/main'
+include { DEEPTOOLS_BAMCOVERAGE as DEEPTOOLS_BAMCOVERAGE_PLUS } from '../../modules/nf-core/deeptools/bamcoverage/main'
+include { DEEPTOOLS_BAMCOVERAGE as DEEPTOOLS_BAMCOVERAGE_MINUS } from '../../modules/nf-core/deeptools/bamcoverage/main'
-include { DREG_PREP } from '../../modules/local/dreg_prep/main'
+include { DREG_PREP } from '../../modules/local/dreg_prep/main'
workflow COVERAGE_GRAPHS {
take:
@@ -21,13 +19,13 @@ workflow COVERAGE_GRAPHS {
main:
- bam = bam_bai.map{ [ it[0], it[1] ] }
+ bam = bam_bai.map { [it[0], it[1]] }
ch_versions = Channel.empty()
ch_genomecov_bam = bam.combine(Channel.from(1))
- BEDTOOLS_GENOMECOV_PLUS (
+ BEDTOOLS_GENOMECOV_PLUS(
ch_genomecov_bam,
sizes,
'bedGraph',
@@ -35,7 +33,7 @@ workflow COVERAGE_GRAPHS {
)
ch_versions = ch_versions.mix(BEDTOOLS_GENOMECOV_PLUS.out.versions.first())
- BEDTOOLS_GENOMECOV_MINUS (
+ BEDTOOLS_GENOMECOV_MINUS(
ch_genomecov_bam,
sizes,
'bedGraph',
@@ -43,14 +41,14 @@ workflow COVERAGE_GRAPHS {
)
ch_versions = ch_versions.mix(BEDTOOLS_GENOMECOV_MINUS.out.versions.first())
- DEEPTOOLS_BAMCOVERAGE_PLUS (
+ DEEPTOOLS_BAMCOVERAGE_PLUS(
bam_bai,
fasta,
fai
)
ch_versions = ch_versions.mix(DEEPTOOLS_BAMCOVERAGE_PLUS.out.versions.first())
- DEEPTOOLS_BAMCOVERAGE_MINUS (
+ DEEPTOOLS_BAMCOVERAGE_MINUS(
bam_bai,
fasta,
fai
@@ -59,17 +57,15 @@ workflow COVERAGE_GRAPHS {
ch_plus_minus = DEEPTOOLS_BAMCOVERAGE_PLUS.out.bigwig.join(DEEPTOOLS_BAMCOVERAGE_MINUS.out.bigwig)
- DREG_PREP (
+ DREG_PREP(
bam_bai,
sizes,
- params.assay_type,
+ params.assay_type
)
emit:
- plus_bedGraph = BEDTOOLS_GENOMECOV_PLUS.out.genomecov
+ plus_bedGraph = BEDTOOLS_GENOMECOV_PLUS.out.genomecov
minus_bedGraph = BEDTOOLS_GENOMECOV_MINUS.out.genomecov
-
- plus_minus = ch_plus_minus
-
- versions = ch_versions
+ plus_minus = ch_plus_minus
+ versions = ch_versions
}
diff --git a/subworkflows/local/dreg_prep/main.nf b/subworkflows/local/dreg_prep/main.nf
index 54c0bff8..942d97ec 100644
--- a/subworkflows/local/dreg_prep/main.nf
+++ b/subworkflows/local/dreg_prep/main.nf
@@ -10,5 +10,4 @@ workflow DREG_PREP {
BEDTOOLS_BAMTOBED(
bam
)
-
}
diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf
index cc5bab21..1e802c27 100644
--- a/subworkflows/local/prepare_genome.nf
+++ b/subworkflows/local/prepare_genome.nf
@@ -2,22 +2,24 @@
// Uncompress and prepare reference genome files
//
-include { GTF2BED } from '../../modules/local/gtf2bed'
+include { GTF2BED } from '../../modules/local/gtf2bed'
include {
- GUNZIP as GUNZIP_FASTA
- GUNZIP as GUNZIP_GTF
- GUNZIP as GUNZIP_GFF
- GUNZIP as GUNZIP_GENE_BED } from '../../modules/nf-core/gunzip/main'
+ GUNZIP as GUNZIP_FASTA ;
+ GUNZIP as GUNZIP_GTF ;
+ GUNZIP as GUNZIP_GFF ;
+ GUNZIP as GUNZIP_GENE_BED
+} from '../../modules/nf-core/gunzip/main'
include {
- UNTAR as UNTAR_BWA_INDEX
- UNTAR as UNTAR_DRAGMAP } from '../../modules/nf-core/untar/main'
-include { GFFREAD } from '../../modules/nf-core/gffread/main'
-include { BWA_INDEX } from '../../modules/nf-core/bwa/index/main'
-include { BWAMEM2_INDEX } from '../../modules/nf-core/bwamem2/index/main'
-include { DRAGMAP_HASHTABLE } from '../../modules/nf-core/dragmap/hashtable/main'
-include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build/main'
-include { CUSTOM_GETCHROMSIZES } from '../../modules/nf-core/custom/getchromsizes/main'
+ UNTAR as UNTAR_BWA_INDEX ;
+ UNTAR as UNTAR_DRAGMAP
+} from '../../modules/nf-core/untar/main'
+include { GFFREAD } from '../../modules/nf-core/gffread/main'
+include { BWA_INDEX } from '../../modules/nf-core/bwa/index/main'
+include { BWAMEM2_INDEX } from '../../modules/nf-core/bwamem2/index/main'
+include { DRAGMAP_HASHTABLE } from '../../modules/nf-core/dragmap/hashtable/main'
+include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build/main'
+include { CUSTOM_GETCHROMSIZES } from '../../modules/nf-core/custom/getchromsizes/main'
workflow PREPARE_GENOME {
take:
@@ -40,9 +42,10 @@ workflow PREPARE_GENOME {
// Uncompress genome fasta file if required
//
if (fasta.endsWith('.gz')) {
- ch_fasta = GUNZIP_FASTA ( [ [:], fasta ] ).gunzip.map { it[1] }
+ ch_fasta = GUNZIP_FASTA([[:], fasta]).gunzip.map { it[1] }
ch_versions = ch_versions.mix(GUNZIP_FASTA.out.versions)
- } else {
+ }
+ else {
ch_fasta = Channel.value(file(fasta))
}
@@ -52,19 +55,22 @@ workflow PREPARE_GENOME {
if (gtf || gff) {
if (gtf) {
if (gtf.endsWith('.gz')) {
- ch_gtf = GUNZIP_GTF ( [ [:], gtf ] ).gunzip.map { it[1] }
+ ch_gtf = GUNZIP_GTF([[:], gtf]).gunzip.map { it[1] }
ch_versions = ch_versions.mix(GUNZIP_GTF.out.versions)
- } else {
+ }
+ else {
ch_gtf = Channel.value(file(gtf))
}
- } else if (gff) {
+ }
+ else if (gff) {
if (gff.endsWith('.gz')) {
- ch_gff = GUNZIP_GFF ( [ [:], gff ] ).gunzip
+ ch_gff = GUNZIP_GFF([[:], gff]).gunzip
ch_versions = ch_versions.mix(GUNZIP_GFF.out.versions)
- } else {
- ch_gff = [ [:], file(gff)]
}
- ch_gtf = GFFREAD ( ch_gff, ch_fasta ).gtf.map { it[1] }
+ else {
+ ch_gff = [[:], file(gff)]
+ }
+ ch_gtf = GFFREAD(ch_gff, ch_fasta).gtf.map { it[1] }
ch_versions = ch_versions.mix(GFFREAD.out.versions)
}
}
@@ -74,23 +80,25 @@ workflow PREPARE_GENOME {
//
if (gene_bed) {
if (gene_bed.endsWith('.gz')) {
- ch_gene_bed = GUNZIP_GENE_BED ( [ [:], gene_bed ] ).gunzip.map { it[1] }
+ ch_gene_bed = GUNZIP_GENE_BED([[:], gene_bed]).gunzip.map { it[1] }
ch_versions = ch_versions.mix(GUNZIP_GENE_BED.out.versions)
- } else {
+ }
+ else {
ch_gene_bed = file(gene_bed)
}
- } else {
- ch_gene_bed = GTF2BED ( ch_gtf ).bed
+ }
+ else {
+ ch_gene_bed = GTF2BED(ch_gtf).bed
ch_versions = ch_versions.mix(GTF2BED.out.versions)
}
//
// Create chromosome sizes file
//
- CUSTOM_GETCHROMSIZES ( ch_fasta.map { [ [:], it ] } )
- ch_fai = CUSTOM_GETCHROMSIZES.out.fai.map { it[1] }
+ CUSTOM_GETCHROMSIZES(ch_fasta.map { [[:], it] })
+ ch_fai = CUSTOM_GETCHROMSIZES.out.fai.map { it[1] }
ch_chrom_sizes = CUSTOM_GETCHROMSIZES.out.sizes.map { it[1] }
- ch_versions = ch_versions.mix(CUSTOM_GETCHROMSIZES.out.versions)
+ ch_versions = ch_versions.mix(CUSTOM_GETCHROMSIZES.out.versions)
//
// Uncompress BWA index or generate from scratch if required
@@ -102,66 +110,76 @@ workflow PREPARE_GENOME {
if ('bwa' in prepare_tool_indices) {
if (bwa_index) {
if (bwa_index.endsWith('.tar.gz')) {
- ch_bwa_index = UNTAR_BWA_INDEX ( [ [:], bwa_index ] ).untar
+ ch_bwa_index = UNTAR_BWA_INDEX([[:], bwa_index]).untar
ch_versions = ch_versions.mix(UNTAR_BWA_INDEX.out.versions)
- } else {
+ }
+ else {
// TODO Give the meta from basename or genome?
- ch_bwa_index = [ [meta: "Genome"], file(bwa_index) ]
+ ch_bwa_index = [[meta: "Genome"], file(bwa_index)]
}
- } else {
- ch_bwa_index = BWA_INDEX ( ch_fasta.map { [ [:], it ] } ).index
+ }
+ else {
+ ch_bwa_index = BWA_INDEX(ch_fasta.map { [[:], it] }).index
ch_versions = ch_versions.mix(BWA_INDEX.out.versions)
}
- } else if ('bwamem2' in prepare_tool_indices) {
+ }
+ else if ('bwamem2' in prepare_tool_indices) {
if (bwamem2_index) {
if (bwamem2_index.endsWith('.tar.gz') || bwamem2_index.endsWith('.tgz')) {
- ch_bwa_index = UNTAR_BWA_INDEX ( [ [:], bwamem2_index ] ).untar
+ ch_bwa_index = UNTAR_BWA_INDEX([[:], bwamem2_index]).untar
ch_versions = ch_versions.mix(UNTAR_BWA_INDEX.out.versions)
- } else {
+ }
+ else {
// TODO Give the meta from basename or genome?
- ch_bwa_index = [ [meta: "Genome"], file(bwamem2_index) ]
+ ch_bwa_index = [[meta: "Genome"], file(bwamem2_index)]
}
- } else {
- ch_bwa_index = BWAMEM2_INDEX ( ch_fasta.map { [ [:], it ] } ).index
+ }
+ else {
+ ch_bwa_index = BWAMEM2_INDEX(ch_fasta.map { [[:], it] }).index
ch_versions = ch_versions.mix(BWAMEM2_INDEX.out.versions)
}
- } else if ('dragmap' in prepare_tool_indices) {
+ }
+ else if ('dragmap' in prepare_tool_indices) {
if (dragmap) {
if (dragmap.endsWith('.tar.gz')) {
- ch_dragmap = UNTAR_DRAGMAP_INDEX ( dragmap ).untar
+ ch_dragmap = UNTAR_DRAGMAP_INDEX(dragmap).untar
ch_versions = ch_versions.mix(UNTAR_DRAGMAP_INDEX.out.versions)
- } else {
+ }
+ else {
// TODO Give the meta from basename or genome?
- ch_dragmap = [ [meta: "Genome"], file(dragmap) ]
+ ch_dragmap = [[meta: "Genome"], file(dragmap)]
}
- } else {
- ch_dragmap = DRAGMAP_HASHTABLE( ch_fasta.map { [ [:], it ] } ).hashmap
+ }
+ else {
+ ch_dragmap = DRAGMAP_HASHTABLE(ch_fasta.map { [[:], it] }).hashmap
ch_versions = ch_versions.mix(DRAGMAP_HASHTABLE.out.versions)
}
- } else if ('bowtie2' in prepare_tool_indices) {
+ }
+ else if ('bowtie2' in prepare_tool_indices) {
if (bowtie2_index) {
if (bowtie2_index.endsWith('.tar.gz')) {
- ch_bowtie2_index = UNTAR_BOWTIE2_INDEX ( bowtie2_index ).untar
+ ch_bowtie2_index = UNTAR_BOWTIE2_INDEX(bowtie2_index).untar
ch_versions = ch_versions.mix(UNTAR_BOWTIE2_INDEX.out.versions)
- } else {
+ }
+ else {
// TODO Give the meta from basename or genome?
- ch_bowtie2_index = [ [meta: "Genome"], file(bowtie2_index) ]
+ ch_bowtie2_index = [[meta: "Genome"], file(bowtie2_index)]
}
- } else {
- ch_bowtie2_index = BOWTIE2_BUILD ( ch_fasta.map { [ [:], it ] } ).index
+ }
+ else {
+ ch_bowtie2_index = BOWTIE2_BUILD(ch_fasta.map { [[:], it] }).index
ch_versions = ch_versions.mix(BOWTIE2_BUILD.out.versions)
}
}
emit:
- fasta = ch_fasta
- fai = ch_fai
- gtf = ch_gtf
- gene_bed = ch_gene_bed
- chrom_sizes = ch_chrom_sizes
- bwa_index = ch_bwa_index
- dragmap = ch_dragmap
+ fasta = ch_fasta
+ fai = ch_fai
+ gtf = ch_gtf
+ gene_bed = ch_gene_bed
+ chrom_sizes = ch_chrom_sizes
+ bwa_index = ch_bwa_index
+ dragmap = ch_dragmap
bowtie2_index = ch_bowtie2_index
-
- versions = ch_versions.ifEmpty(null)
+ versions = ch_versions.ifEmpty(null)
}
diff --git a/subworkflows/local/quality_control.nf b/subworkflows/local/quality_control.nf
index ad24c7d9..9169d4cd 100644
--- a/subworkflows/local/quality_control.nf
+++ b/subworkflows/local/quality_control.nf
@@ -1,8 +1,8 @@
-include { PRESEQ_CCURVE } from '../../modules/nf-core/preseq/ccurve/main'
+include { PRESEQ_CCURVE } from '../../modules/nf-core/preseq/ccurve/main'
include { PRESEQ_LCEXTRAP } from '../../modules/nf-core/preseq/lcextrap/main'
-include { BBMAP_PILEUP } from '../../modules/nf-core/bbmap/pileup/main'
+include { BBMAP_PILEUP } from '../../modules/nf-core/bbmap/pileup/main'
-include { BAM_RSEQC } from '../../subworkflows/nf-core/bam_rseqc'
+include { BAM_RSEQC } from '../../subworkflows/nf-core/bam_rseqc'
workflow QUALITY_CONTROL {
take:
@@ -11,37 +11,34 @@ workflow QUALITY_CONTROL {
main:
- bam = bam_bai.map{ [ it[0], it[1] ] }
+ bam = bam_bai.map { [it[0], it[1]] }
ch_versions = Channel.empty()
- PRESEQ_CCURVE ( bam )
+ PRESEQ_CCURVE(bam)
ch_versions = ch_versions.mix(PRESEQ_CCURVE.out.versions.first())
- PRESEQ_LCEXTRAP ( bam )
+ PRESEQ_LCEXTRAP(bam)
ch_versions = ch_versions.mix(PRESEQ_LCEXTRAP.out.versions.first())
// TODO Set this in a param?
rseqc_modules = ['read_duplication', 'read_distribution', 'infer_experiment']
- BAM_RSEQC ( bam_bai, bed, rseqc_modules )
+ BAM_RSEQC(bam_bai, bed, rseqc_modules)
ch_versions = ch_versions.mix(BAM_RSEQC.out.versions)
- BBMAP_PILEUP ( bam )
+ BBMAP_PILEUP(bam)
ch_versions = ch_versions.mix(BBMAP_PILEUP.out.versions.first())
emit:
- preseq_ccurve = PRESEQ_CCURVE.out.c_curve
- preseq_lcextrap = PRESEQ_LCEXTRAP.out.lc_extrap
-
- inferexperiment_txt = BAM_RSEQC.out.inferexperiment_txt
- readdistribution_txt = BAM_RSEQC.out.readdistribution_txt
+ preseq_ccurve = PRESEQ_CCURVE.out.c_curve
+ preseq_lcextrap = PRESEQ_LCEXTRAP.out.lc_extrap
+ inferexperiment_txt = BAM_RSEQC.out.inferexperiment_txt
+ readdistribution_txt = BAM_RSEQC.out.readdistribution_txt
readduplication_seq_xls = BAM_RSEQC.out.readduplication_seq_xls
readduplication_pos_xls = BAM_RSEQC.out.readduplication_pos_xls
- readduplication_pdf = BAM_RSEQC.out.readduplication_pdf
+ readduplication_pdf = BAM_RSEQC.out.readduplication_pdf
readduplication_rscript = BAM_RSEQC.out.readduplication_rscript
-
- pileup_stats = BBMAP_PILEUP.out.covstats
- pileup_hist = BBMAP_PILEUP.out.hist
-
- versions = ch_versions
+ pileup_stats = BBMAP_PILEUP.out.covstats
+ pileup_hist = BBMAP_PILEUP.out.hist
+ versions = ch_versions
}
diff --git a/subworkflows/local/transcript_identification/main.nf b/subworkflows/local/transcript_identification/main.nf
index 890f5579..537c8552 100644
--- a/subworkflows/local/transcript_identification/main.nf
+++ b/subworkflows/local/transcript_identification/main.nf
@@ -37,7 +37,7 @@ workflow TRANSCRIPT_INDENTIFICATION {
homer_peaks = Channel.empty()
homer_tagdir = Channel.empty()
if (params.assay_type == "GROseq") {
- group_bam = group_bam_bai.map { meta, bam, bai -> [meta, bam] }
+ group_bam = group_bam_bai.map { meta, bam, _bai -> [meta, bam] }
HOMER_GROSEQ(group_bam, fasta, uniqmap)
ch_identification_bed = ch_identification_bed.mix(HOMER_GROSEQ.out.bed)
homer_peaks = HOMER_GROSEQ.out.peaks
@@ -78,7 +78,7 @@ workflow TRANSCRIPT_INDENTIFICATION {
// TODO Tests don't seem to hit this because there's no bidirectional_TREs
// Need to collect all of the beds for each chromosome/sample and concatenate them
// Nextflow makes this super easy
- def ch_bidirectional_tres = PINTS_CALLER.out.unidirectional_TREs.groupTuple(by: [0]).map { meta, beds ->
+ ch_bidirectional_tres = PINTS_CALLER.out.unidirectional_TREs.groupTuple(by: [0]).map { meta, beds ->
[meta, beds.flatten()]
}
@@ -106,7 +106,7 @@ workflow TRANSCRIPT_INDENTIFICATION {
}
ch_identification_bed
- .filter { meta, bed -> bed.size() > 0 }
+ .filter { _meta, bed -> bed.size() > 0 }
.set { ch_identification_bed_clean }
emit:
diff --git a/subworkflows/local/utils_nfcore_nascent_pipeline/main.nf b/subworkflows/local/utils_nfcore_nascent_pipeline/main.nf
index bf28cfc1..9a421fa5 100644
--- a/subworkflows/local/utils_nfcore_nascent_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_nascent_pipeline/main.nf
@@ -8,14 +8,14 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin'
-include { paramsSummaryMap } from 'plugin/nf-schema'
-include { samplesheetToList } from 'plugin/nf-schema'
-include { completionEmail } from '../../nf-core/utils_nfcore_pipeline'
-include { completionSummary } from '../../nf-core/utils_nfcore_pipeline'
-include { imNotification } from '../../nf-core/utils_nfcore_pipeline'
-include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline'
-include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline'
+include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin'
+include { paramsSummaryMap } from 'plugin/nf-schema'
+include { samplesheetToList } from 'plugin/nf-schema'
+include { completionEmail } from '../../nf-core/utils_nfcore_pipeline'
+include { completionSummary } from '../../nf-core/utils_nfcore_pipeline'
+include { imNotification } from '../../nf-core/utils_nfcore_pipeline'
+include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline'
+include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -24,7 +24,6 @@ include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipelin
*/
workflow PIPELINE_INITIALISATION {
-
take:
version // boolean: Display version and exit
validate_params // boolean: Boolean whether to validate parameters against the schema at runtime
@@ -40,7 +39,7 @@ workflow PIPELINE_INITIALISATION {
//
// Print version and exit if required and dump pipeline parameters to JSON file
//
- UTILS_NEXTFLOW_PIPELINE (
+ UTILS_NEXTFLOW_PIPELINE(
version,
true,
outdir,
@@ -50,7 +49,7 @@ workflow PIPELINE_INITIALISATION {
//
// Validate parameters and generate parameter summary to stdout
//
- UTILS_NFSCHEMA_PLUGIN (
+ UTILS_NFSCHEMA_PLUGIN(
workflow,
validate_params,
null
@@ -59,7 +58,7 @@ workflow PIPELINE_INITIALISATION {
//
// Check config provided to the pipeline
//
- UTILS_NFCORE_PIPELINE (
+ UTILS_NFCORE_PIPELINE(
nextflow_cli_args
)
@@ -74,21 +73,20 @@ workflow PIPELINE_INITIALISATION {
Channel
.fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
- .map {
- meta, fastq_1, fastq_2 ->
- if (!fastq_2) {
- return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ]
- } else {
- return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ]
- }
+ .map { meta, fastq_1, fastq_2 ->
+ if (!fastq_2) {
+ return [meta.id, meta + [single_end: true], [fastq_1]]
+ }
+ else {
+ return [meta.id, meta + [single_end: false], [fastq_1, fastq_2]]
+ }
}
.groupTuple()
.map { samplesheet ->
validateInputSamplesheet(samplesheet)
}
- .map {
- meta, fastqs ->
- return [ meta, fastqs.flatten() ]
+ .map { meta, fastqs ->
+ return [meta, fastqs.flatten()]
}
.set { ch_samplesheet }
@@ -104,7 +102,6 @@ workflow PIPELINE_INITIALISATION {
*/
workflow PIPELINE_COMPLETION {
-
take:
email // string: email address
email_on_fail // string: email address sent on pipeline failure
@@ -130,7 +127,7 @@ workflow PIPELINE_COMPLETION {
plaintext_email,
outdir,
monochrome_logs,
- multiqc_reports.getVal(),
+ multiqc_reports.getVal()
)
}
@@ -141,7 +138,7 @@ workflow PIPELINE_COMPLETION {
}
workflow.onError {
- log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting"
+ log.error("Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting")
}
}
@@ -164,20 +161,20 @@ def validateInputSamplesheet(input) {
def (metas, fastqs) = input[1..2]
// Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
- def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1
+ def endedness_ok = metas.collect { meta -> meta.single_end }.unique().size == 1
if (!endedness_ok) {
error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}")
}
- return [ metas[0], fastqs ]
+ return [metas[0], fastqs]
}
//
// Get attribute from genome config file e.g. fasta
//
def getGenomeAttribute(attribute) {
if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
- if (params.genomes[ params.genome ].containsKey(attribute)) {
- return params.genomes[ params.genome ][ attribute ]
+ if (params.genomes[params.genome].containsKey(attribute)) {
+ return params.genomes[params.genome][attribute]
}
}
return null
@@ -188,11 +185,7 @@ def getGenomeAttribute(attribute) {
//
def genomeExistsError() {
if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
- def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
- " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
- " Currently, the available genome keys are:\n" +
- " ${params.genomes.keySet().join(", ")}\n" +
- "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+ def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + " Currently, the available genome keys are:\n" + " ${params.genomes.keySet().join(", ")}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
error(error_string)
}
}
@@ -272,10 +265,13 @@ def methodsDescriptionText(mqc_methods_yaml) {
def temp_doi_ref = ""
def manifest_doi = meta.manifest_map.doi.tokenize(",")
manifest_doi.each { doi_ref ->
- temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), "
+ temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), "
}
meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2)
- } else meta["doi_text"] = ""
+ }
+ else {
+ meta["doi_text"] = ""
+ }
meta["nodoi_text"] = meta.manifest_map.doi ? "" : "If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. "
// Tool references
@@ -288,9 +284,8 @@ def methodsDescriptionText(mqc_methods_yaml) {
def methods_text = mqc_methods_yaml.text
- def engine = new groovy.text.SimpleTemplateEngine()
+ def engine = new groovy.text.SimpleTemplateEngine()
def description_html = engine.createTemplate(methods_text).make(meta)
return description_html.toString()
}
-
diff --git a/workflows/nascent.nf b/workflows/nascent.nf
index bb1eb1b9..724bf1bb 100644
--- a/workflows/nascent.nf
+++ b/workflows/nascent.nf
@@ -4,40 +4,38 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-include { BED2SAF } from '../modules/local/bed2saf'
-
-include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome'
-include { ALIGN_BWAMEM2 } from '../subworkflows/local/align_bwamem2/main'
-include { ALIGN_DRAGMAP } from '../subworkflows/local/align_dragmap/main'
-include { QUALITY_CONTROL } from '../subworkflows/local/quality_control.nf'
-include { COVERAGE_GRAPHS } from '../subworkflows/local/coverage_graphs.nf'
-include { TRANSCRIPT_INDENTIFICATION } from '../subworkflows/local/transcript_identification'
-
-include { FASTP } from '../modules/nf-core/fastp/main'
-include {
- UNTAR as UNTAR_HISAT2_INDEX
- UNTAR as UNTAR_STAR_INDEX
-} from '../modules/nf-core/untar/main'
-include { STAR_GENOMEGENERATE } from '../modules/nf-core/star/genomegenerate/main'
-include {
- SUBREAD_FEATURECOUNTS as SUBREAD_FEATURECOUNTS_GENE
- SUBREAD_FEATURECOUNTS as SUBREAD_FEATURECOUNTS_PREDICTED } from '../modules/nf-core/subread/featurecounts/main'
-
-include { FASTQC } from '../modules/nf-core/fastqc/main'
-include { MULTIQC } from '../modules/nf-core/multiqc/main'
-include { paramsSummaryMap } from 'plugin/nf-schema'
-include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_nascent_pipeline'
+include { BED2SAF } from '../modules/local/bed2saf'
+
+include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome'
+include { ALIGN_BWAMEM2 } from '../subworkflows/local/align_bwamem2/main'
+include { ALIGN_DRAGMAP } from '../subworkflows/local/align_dragmap/main'
+include { QUALITY_CONTROL } from '../subworkflows/local/quality_control.nf'
+include { COVERAGE_GRAPHS } from '../subworkflows/local/coverage_graphs.nf'
+include { TRANSCRIPT_INDENTIFICATION } from '../subworkflows/local/transcript_identification'
+
+include { FASTP } from '../modules/nf-core/fastp/main'
+include { UNTAR as UNTAR_HISAT2_INDEX } from '../modules/nf-core/untar/main'
+include { UNTAR as UNTAR_STAR_INDEX } from '../modules/nf-core/untar/main'
+include { STAR_GENOMEGENERATE } from '../modules/nf-core/star/genomegenerate/main'
+include { SUBREAD_FEATURECOUNTS as SUBREAD_FEATURECOUNTS_GENE } from '../modules/nf-core/subread/featurecounts/main'
+include { SUBREAD_FEATURECOUNTS as SUBREAD_FEATURECOUNTS_PREDICTED } from '../modules/nf-core/subread/featurecounts/main'
+
+
+include { FASTQC } from '../modules/nf-core/fastqc/main'
+include { MULTIQC } from '../modules/nf-core/multiqc/main'
+include { paramsSummaryMap } from 'plugin/nf-schema'
+include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_nascent_pipeline'
//
// SUBWORKFLOW: Consisting entirely of nf-core/modules
//
-include { FASTQ_ALIGN_BWA } from '../subworkflows/nf-core/fastq_align_bwa/main'
-include { FASTQ_ALIGN_BOWTIE2 } from '../subworkflows/nf-core/fastq_align_bowtie2/main'
-include { FASTQ_ALIGN_HISAT2 } from '../subworkflows/nf-core/fastq_align_hisat2/main'
-include { FASTQ_ALIGN_STAR } from '../subworkflows/nf-core/fastq_align_star/main'
-include { BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS } from '../subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main'
+include { FASTQ_ALIGN_BWA } from '../subworkflows/nf-core/fastq_align_bwa/main'
+include { FASTQ_ALIGN_BOWTIE2 } from '../subworkflows/nf-core/fastq_align_bowtie2/main'
+include { FASTQ_ALIGN_HISAT2 } from '../subworkflows/nf-core/fastq_align_hisat2/main'
+include { FASTQ_ALIGN_STAR } from '../subworkflows/nf-core/fastq_align_star/main'
+include { BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS } from '../subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -46,9 +44,8 @@ include { BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS } from '../subworkflows/nf-core/bam_
*/
workflow NASCENT {
-
take:
- ch_samplesheet // channel: samplesheet read in from --input
+ ch_samplesheet // channel: samplesheet read in from --input
ch_fasta
ch_gtf
ch_gff
@@ -61,7 +58,6 @@ workflow NASCENT {
ch_star_index
ch_uniqmap
-
main:
ch_versions = Channel.empty()
@@ -72,8 +68,10 @@ workflow NASCENT {
// HACK Rework this because of nf-validation
def prepareToolIndices = []
- if (!params.skip_alignment) { prepareToolIndices << params.aligner }
- PREPARE_GENOME (
+ if (!params.skip_alignment) {
+ prepareToolIndices << params.aligner
+ }
+ PREPARE_GENOME(
prepareToolIndices,
ch_fasta,
ch_gtf,
@@ -83,26 +81,27 @@ workflow NASCENT {
ch_bwamem2_index,
ch_dragmap,
ch_bowtie2_index,
- ch_hisat2_index,
+ ch_hisat2_index
)
ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)
- ch_fasta = PREPARE_GENOME.out.fasta.map{ fasta -> [ [ id:fasta.baseName ], fasta ] }
+ ch_fasta = PREPARE_GENOME.out.fasta.map { fasta -> [[id: fasta.baseName], fasta] }
//
// MODULE: Run FastQC
//
- FASTQC (
+ FASTQC(
ch_samplesheet
)
- ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]})
+ ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect { it[1] })
ch_versions = ch_versions.mix(FASTQC.out.versions.first())
ch_reads = Channel.empty()
- if(!params.skip_trimming) {
- FASTP ( ch_samplesheet, [], false, false, false )
+ if (!params.skip_trimming) {
+ FASTP(ch_samplesheet, [], false, false, false)
ch_reads = FASTP.out.reads
ch_versions = ch_versions.mix(FASTP.out.versions.first())
- } else {
+ }
+ else {
ch_reads = ch_samplesheet
}
@@ -119,11 +118,11 @@ workflow NASCENT {
ch_aligner_clustering_multiqc = Channel.empty()
ch_bowtie2_multiqc = Channel.empty()
if (!params.skip_alignment && params.aligner == 'bwa') {
- FASTQ_ALIGN_BWA (
+ FASTQ_ALIGN_BWA(
ch_reads,
PREPARE_GENOME.out.bwa_index,
false,
- ch_fasta,
+ ch_fasta
)
ch_genome_bam = FASTQ_ALIGN_BWA.out.bam
ch_genome_bai = FASTQ_ALIGN_BWA.out.bai
@@ -132,12 +131,13 @@ workflow NASCENT {
ch_samtools_idxstats = FASTQ_ALIGN_BWA.out.idxstats
ch_versions = ch_versions.mix(FASTQ_ALIGN_BWA.out.versions.first())
- } else if (!params.skip_alignment && params.aligner == 'bwamem2') {
- ALIGN_BWAMEM2 (
+ }
+ else if (!params.skip_alignment && params.aligner == 'bwamem2') {
+ ALIGN_BWAMEM2(
ch_reads,
PREPARE_GENOME.out.bwa_index,
false,
- ch_fasta,
+ ch_fasta
)
ch_genome_bam = ALIGN_BWAMEM2.out.bam
ch_genome_bai = ALIGN_BWAMEM2.out.bai
@@ -146,12 +146,13 @@ workflow NASCENT {
ch_samtools_idxstats = ALIGN_BWAMEM2.out.idxstats
ch_versions = ch_versions.mix(ALIGN_BWAMEM2.out.versions)
- } else if (!params.skip_alignment && params.aligner == 'dragmap') {
- ALIGN_DRAGMAP (
+ }
+ else if (!params.skip_alignment && params.aligner == 'dragmap') {
+ ALIGN_DRAGMAP(
ch_reads,
PREPARE_GENOME.out.dragmap,
false,
- ch_fasta,
+ ch_fasta
)
ch_genome_bam = ALIGN_DRAGMAP.out.bam
ch_genome_bai = ALIGN_DRAGMAP.out.bai
@@ -160,13 +161,14 @@ workflow NASCENT {
ch_samtools_idxstats = ALIGN_DRAGMAP.out.idxstats
ch_versions = ch_versions.mix(ALIGN_DRAGMAP.out.versions)
- } else if (!params.skip_alignment && params.aligner == 'bowtie2') {
- FASTQ_ALIGN_BOWTIE2 (
+ }
+ else if (!params.skip_alignment && params.aligner == 'bowtie2') {
+ FASTQ_ALIGN_BOWTIE2(
ch_reads,
PREPARE_GENOME.out.bowtie2_index,
false,
false,
- ch_fasta,
+ ch_fasta
)
ch_genome_bam = FASTQ_ALIGN_BOWTIE2.out.bam
ch_genome_bai = FASTQ_ALIGN_BOWTIE2.out.bai
@@ -176,20 +178,22 @@ workflow NASCENT {
ch_bowtie2_multiqc = FASTQ_ALIGN_BOWTIE2.out.log_out
ch_versions = ch_versions.mix(FASTQ_ALIGN_BOWTIE2.out.versions)
- } else if (!params.skip_alignment && params.aligner == 'hisat2') {
+ }
+ else if (!params.skip_alignment && params.aligner == 'hisat2') {
if (ch_hisat2_index.endsWith('.tar.gz')) {
- ch_hisat2_index = UNTAR_HISAT2_INDEX ( [ [:], ch_hisat2_index ] ).untar
+ ch_hisat2_index = UNTAR_HISAT2_INDEX([[:], ch_hisat2_index]).untar
ch_versions = ch_versions.mix(UNTAR_HISAT2_INDEX.out.versions)
- } else {
+ }
+ else {
// TODO Give the meta from basename or genome?
- ch_hisat2_index = [ [meta: "Genome"], file(ch_hisat2_index) ]
+ ch_hisat2_index = [[meta: "Genome"], file(ch_hisat2_index)]
}
- FASTQ_ALIGN_HISAT2 (
+ FASTQ_ALIGN_HISAT2(
ch_reads,
ch_hisat2_index,
- [[:],[]],
- ch_fasta,
+ [[:], []],
+ ch_fasta
)
ch_genome_bam = FASTQ_ALIGN_HISAT2.out.bam
ch_genome_bai = FASTQ_ALIGN_HISAT2.out.bai
@@ -199,42 +203,45 @@ workflow NASCENT {
ch_HISAT2_multiqc = FASTQ_ALIGN_HISAT2.out.summary
ch_versions = ch_versions.mix(FASTQ_ALIGN_HISAT2.out.versions)
- } else if (!params.skip_alignment && params.aligner == 'star') {
- if(!ch_star_index) {
- ch_star_index = STAR_GENOMEGENERATE (
+ }
+ else if (!params.skip_alignment && params.aligner == 'star') {
+ if (!ch_star_index) {
+ ch_star_index = STAR_GENOMEGENERATE(
ch_fasta,
PREPARE_GENOME.out.gtf.map { [[:], it] }
).index
- } else if (ch_star_index.endsWith('.tar.gz')) {
- ch_star_index = UNTAR_STAR_INDEX ( [ [:], ch_star_index ] ).untar
+ }
+ else if (ch_star_index.endsWith('.tar.gz')) {
+ ch_star_index = UNTAR_STAR_INDEX([[:], ch_star_index]).untar
ch_versions = ch_versions.mix(UNTAR_STAR_INDEX.out.versions)
- } else {
+ }
+ else {
// TODO Give the meta from basename or genome?
- ch_star_index = [ [meta: "Genome"], file(ch_star_index) ]
+ ch_star_index = [[meta: "Genome"], file(ch_star_index)]
}
- FASTQ_ALIGN_STAR (
+ FASTQ_ALIGN_STAR(
ch_reads,
ch_star_index,
- PREPARE_GENOME.out.gtf.map { [ [:], it ] },
+ PREPARE_GENOME.out.gtf.map { [[:], it] },
false,
'',
- '', // TODO params.seq_center ?:
+ '',
ch_fasta,
- Channel.of([[:], []]),
+ Channel.of([[:], []])
)
- ch_genome_bam = FASTQ_ALIGN_STAR.out.bam
- ch_genome_bai = FASTQ_ALIGN_STAR.out.bai
+ ch_genome_bam = FASTQ_ALIGN_STAR.out.bam
+ ch_genome_bai = FASTQ_ALIGN_STAR.out.bai
ch_transcriptome_bam = FASTQ_ALIGN_STAR.out.bam_transcript
- ch_star_log = FASTQ_ALIGN_STAR.out.log_final
- ch_multiqc_files = ch_multiqc_files.mix(FASTQ_ALIGN_STAR.out.stats.collect{it[1]})
- ch_multiqc_files = ch_multiqc_files.mix(FASTQ_ALIGN_STAR.out.flagstat.collect{it[1]})
- ch_multiqc_files = ch_multiqc_files.mix(FASTQ_ALIGN_STAR.out.idxstats.collect{it[1]})
- ch_multiqc_files = ch_multiqc_files.mix(ch_star_log.collect{it[1]})
+ ch_star_log = FASTQ_ALIGN_STAR.out.log_final
+ ch_multiqc_files = ch_multiqc_files.mix(FASTQ_ALIGN_STAR.out.stats.collect { it[1] })
+ ch_multiqc_files = ch_multiqc_files.mix(FASTQ_ALIGN_STAR.out.flagstat.collect { it[1] })
+ ch_multiqc_files = ch_multiqc_files.mix(FASTQ_ALIGN_STAR.out.idxstats.collect { it[1] })
+ ch_multiqc_files = ch_multiqc_files.mix(ch_star_log.collect { it[1] })
}
- if(params.with_umi) {
- BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS (
+ if (params.with_umi) {
+ BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS(
ch_genome_bam.join(ch_genome_bai, by: [0]),
params.umitools_dedup_stats
)
@@ -249,13 +256,13 @@ workflow NASCENT {
ch_genome_bam_bai = ch_genome_bam.join(ch_genome_bai, by: [0], remainder: true)
- QUALITY_CONTROL (
+ QUALITY_CONTROL(
ch_genome_bam_bai,
PREPARE_GENOME.out.gene_bed
)
ch_versions = ch_versions.mix(QUALITY_CONTROL.out.versions)
- COVERAGE_GRAPHS (
+ COVERAGE_GRAPHS(
ch_genome_bam_bai,
PREPARE_GENOME.out.chrom_sizes,
PREPARE_GENOME.out.fasta,
@@ -266,31 +273,33 @@ workflow NASCENT {
//
// SUBWORKFLOW: Transcript indetification
//
- ch_genome_bam.map {
- meta, bam ->
- fmeta = meta.findAll { it.key != 'read_group' }
- // Split and take the first element
- fmeta.id = fmeta.id.split('_')[0]
- [ fmeta, bam ] }
+ ch_genome_bam
+ .map { meta, bam ->
+ fmeta = meta.findAll { it.key != 'read_group' }
+ // Split and take the first element
+ fmeta.id = fmeta.id.split('_')[0]
+ [fmeta, bam]
+ }
.groupTuple(by: [0])
- .map { it -> [ it[0], it[1].flatten() ] }
+ .map { it -> [it[0], it[1].flatten()] }
.set { ch_group_bam }
// Group the index files with bams
- ch_genome_bai.map {
- meta, bai ->
- fmeta = meta.findAll { it.key != 'read_group' }
- // Split and take the first element
- fmeta.id = fmeta.id.split('_')[0]
- [ fmeta, bai ] }
+ ch_genome_bai
+ .map { meta, bai ->
+ fmeta = meta.findAll { it.key != 'read_group' }
+ // Split and take the first element
+ fmeta.id = fmeta.id.split('_')[0]
+ [fmeta, bai]
+ }
.groupTuple(by: [0])
- .map { it -> [ it[0], it[1].flatten() ] }
+ .map { it -> [it[0], it[1].flatten()] }
.set { ch_group_bai }
ch_group_bam_bai = ch_group_bam.join(ch_group_bai, by: [0])
ch_gxf = ch_gff ? ch_gff : PREPARE_GENOME.out.gtf
- TRANSCRIPT_INDENTIFICATION (
+ TRANSCRIPT_INDENTIFICATION(
ch_group_bam_bai,
ch_gxf,
PREPARE_GENOME.out.fasta,
@@ -302,16 +311,16 @@ workflow NASCENT {
ch_homer_multiqc = ch_homer_multiqc.mix(TRANSCRIPT_INDENTIFICATION.out.homer_tagdir)
ch_versions = ch_versions.mix(TRANSCRIPT_INDENTIFICATION.out.versions)
- SUBREAD_FEATURECOUNTS_PREDICTED (
+ SUBREAD_FEATURECOUNTS_PREDICTED(
ch_group_bam.combine(
- BED2SAF (
+ BED2SAF(
TRANSCRIPT_INDENTIFICATION.out.transcript_beds
).saf.map { it[1] }
)
)
ch_versions = ch_versions.mix(SUBREAD_FEATURECOUNTS_PREDICTED.out.versions.first())
- SUBREAD_FEATURECOUNTS_GENE (
+ SUBREAD_FEATURECOUNTS_GENE(
ch_group_bam.combine(PREPARE_GENOME.out.gtf)
)
ch_versions = ch_versions.mix(SUBREAD_FEATURECOUNTS_GENE.out.versions.first())
@@ -322,34 +331,41 @@ workflow NASCENT {
softwareVersionsToYAML(ch_versions)
.collectFile(
storeDir: "${params.outdir}/pipeline_info",
- name: 'nf_core_' + 'nascent_software_' + 'mqc_' + 'versions.yml',
+ name: 'nf_core_' + 'nascent_software_' + 'mqc_' + 'versions.yml',
sort: true,
newLine: true
- ).set { ch_collated_versions }
+ )
+ .set { ch_collated_versions }
//
// MODULE: MultiQC
//
- ch_multiqc_config = Channel.fromPath(
- "$projectDir/assets/multiqc_config.yml", checkIfExists: true)
- ch_multiqc_custom_config = params.multiqc_config ?
- Channel.fromPath(params.multiqc_config, checkIfExists: true) :
- Channel.empty()
- ch_multiqc_logo = params.multiqc_logo ?
- Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
- Channel.empty()
-
- summary_params = paramsSummaryMap(
- workflow, parameters_schema: "nextflow_schema.json")
+ ch_multiqc_config = Channel.fromPath(
+ "${projectDir}/assets/multiqc_config.yml",
+ checkIfExists: true
+ )
+ ch_multiqc_custom_config = params.multiqc_config
+ ? Channel.fromPath(params.multiqc_config, checkIfExists: true)
+ : Channel.empty()
+ ch_multiqc_logo = params.multiqc_logo
+ ? Channel.fromPath(params.multiqc_logo, checkIfExists: true)
+ : Channel.empty()
+
+ summary_params = paramsSummaryMap(
+ workflow,
+ parameters_schema: "nextflow_schema.json"
+ )
ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
ch_multiqc_files = ch_multiqc_files.mix(
- ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
- ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
- file(params.multiqc_methods_description, checkIfExists: true) :
- file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
- ch_methods_description = Channel.value(
- methodsDescriptionText(ch_multiqc_custom_methods_description))
+ ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')
+ )
+ ch_multiqc_custom_methods_description = params.multiqc_methods_description
+ ? file(params.multiqc_methods_description, checkIfExists: true)
+ : file("${projectDir}/assets/methods_description_template.yml", checkIfExists: true)
+ ch_methods_description = Channel.value(
+ methodsDescriptionText(ch_multiqc_custom_methods_description)
+ )
ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
ch_multiqc_files = ch_multiqc_files.mix(
@@ -359,38 +375,32 @@ workflow NASCENT {
)
)
- ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
- ch_multiqc_files = ch_multiqc_files.mix(ch_bowtie2_multiqc.collect{it[1]}.ifEmpty([]))
- ch_multiqc_files = ch_multiqc_files.mix(ch_samtools_stats.collect{it[1]}.ifEmpty([]))
- ch_multiqc_files = ch_multiqc_files.mix(ch_samtools_flagstat.collect{it[1]}.ifEmpty([]))
- ch_multiqc_files = ch_multiqc_files.mix(ch_samtools_idxstats.collect{it[1]}.ifEmpty([]))
- ch_multiqc_files = ch_multiqc_files.mix(QUALITY_CONTROL.out.preseq_ccurve.collect{it[1]}.ifEmpty([]))
- ch_multiqc_files = ch_multiqc_files.mix(QUALITY_CONTROL.out.preseq_lcextrap.collect{it[1]}.ifEmpty([]))
- ch_multiqc_files = ch_multiqc_files.mix(QUALITY_CONTROL.out.readdistribution_txt.collect{it[1]}.ifEmpty([]))
- ch_multiqc_files = ch_multiqc_files.mix(QUALITY_CONTROL.out.readduplication_seq_xls.collect{it[1]}.ifEmpty([]))
- ch_multiqc_files = ch_multiqc_files.mix(QUALITY_CONTROL.out.readduplication_pos_xls.collect{it[1]}.ifEmpty([]))
- ch_multiqc_files = ch_multiqc_files.mix(QUALITY_CONTROL.out.inferexperiment_txt.collect{it[1]}.ifEmpty([]))
- ch_multiqc_files = ch_multiqc_files.mix(ch_grohmm_multiqc.collect{it[1]}.ifEmpty([]))
- ch_multiqc_files = ch_multiqc_files.mix(ch_homer_multiqc.collect{it[1]}.ifEmpty([]))
- ch_multiqc_files = ch_multiqc_files.mix(SUBREAD_FEATURECOUNTS_PREDICTED.out.summary.collect{it[1]}.ifEmpty([]))
- ch_multiqc_files = ch_multiqc_files.mix(SUBREAD_FEATURECOUNTS_GENE.out.summary.collect{it[1]}.ifEmpty([]))
-
- MULTIQC (
+ ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect { it[1] }.ifEmpty([]))
+ ch_multiqc_files = ch_multiqc_files.mix(ch_bowtie2_multiqc.collect { it[1] }.ifEmpty([]))
+ ch_multiqc_files = ch_multiqc_files.mix(ch_samtools_stats.collect { it[1] }.ifEmpty([]))
+ ch_multiqc_files = ch_multiqc_files.mix(ch_samtools_flagstat.collect { it[1] }.ifEmpty([]))
+ ch_multiqc_files = ch_multiqc_files.mix(ch_samtools_idxstats.collect { it[1] }.ifEmpty([]))
+ ch_multiqc_files = ch_multiqc_files.mix(QUALITY_CONTROL.out.preseq_ccurve.collect { it[1] }.ifEmpty([]))
+ ch_multiqc_files = ch_multiqc_files.mix(QUALITY_CONTROL.out.preseq_lcextrap.collect { it[1] }.ifEmpty([]))
+ ch_multiqc_files = ch_multiqc_files.mix(QUALITY_CONTROL.out.readdistribution_txt.collect { it[1] }.ifEmpty([]))
+ ch_multiqc_files = ch_multiqc_files.mix(QUALITY_CONTROL.out.readduplication_seq_xls.collect { it[1] }.ifEmpty([]))
+ ch_multiqc_files = ch_multiqc_files.mix(QUALITY_CONTROL.out.readduplication_pos_xls.collect { it[1] }.ifEmpty([]))
+ ch_multiqc_files = ch_multiqc_files.mix(QUALITY_CONTROL.out.inferexperiment_txt.collect { it[1] }.ifEmpty([]))
+ ch_multiqc_files = ch_multiqc_files.mix(ch_grohmm_multiqc.collect { it[1] }.ifEmpty([]))
+ ch_multiqc_files = ch_multiqc_files.mix(ch_homer_multiqc.collect { it[1] }.ifEmpty([]))
+ ch_multiqc_files = ch_multiqc_files.mix(SUBREAD_FEATURECOUNTS_PREDICTED.out.summary.collect { it[1] }.ifEmpty([]))
+ ch_multiqc_files = ch_multiqc_files.mix(SUBREAD_FEATURECOUNTS_GENE.out.summary.collect { it[1] }.ifEmpty([]))
+
+ MULTIQC(
ch_multiqc_files.collect(),
ch_multiqc_config.toList(),
ch_multiqc_custom_config.toList(),
ch_multiqc_logo.toList(),
[],
- [],
+ []
)
- emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
- versions = ch_versions // channel: [ path(versions.yml) ]
-
+ emit:
+ multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
+ versions = ch_versions // channel: [ path(versions.yml) ]
}
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- THE END
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
diff --git a/workflows/tests/aligner/bowtie2.nf.test b/workflows/tests/aligner/bowtie2.nf.test
index add662c6..4f91e553 100644
--- a/workflows/tests/aligner/bowtie2.nf.test
+++ b/workflows/tests/aligner/bowtie2.nf.test
@@ -27,7 +27,7 @@ nextflow_pipeline {
// Number of tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
- removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+ removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml"),
// All stable path name
stable_name,
// All files with stable contents
diff --git a/workflows/tests/aligner/bowtie2.nf.test.snap b/workflows/tests/aligner/bowtie2.nf.test.snap
index 7ea4e747..804a5398 100644
--- a/workflows/tests/aligner/bowtie2.nf.test.snap
+++ b/workflows/tests/aligner/bowtie2.nf.test.snap
@@ -172,7 +172,7 @@
"multiqc/multiqc_data/samtools_alignment_plot.txt",
"multiqc/multiqc_report.html",
"pipeline_info",
- "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+ "pipeline_info/nf_core_nascent_software_mqc_versions.yml",
"preprocessing",
"preprocessing/fastp",
"preprocessing/fastp/cd4_REP1.trimmed.fastp.html",
@@ -324,4 +324,4 @@
},
"timestamp": "2024-12-18T07:25:45.87987"
}
-}
\ No newline at end of file
+}
diff --git a/workflows/tests/aligner/bwa.nf.test b/workflows/tests/aligner/bwa.nf.test
index 0e1f6f66..ed8e201a 100644
--- a/workflows/tests/aligner/bwa.nf.test
+++ b/workflows/tests/aligner/bwa.nf.test
@@ -28,7 +28,7 @@ nextflow_pipeline {
// Number of tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
- removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+ removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml"),
// All stable path name
stable_name,
// All files with stable contents
diff --git a/workflows/tests/aligner/bwa.nf.test.snap b/workflows/tests/aligner/bwa.nf.test.snap
index 8f7e1743..5bb2633d 100644
--- a/workflows/tests/aligner/bwa.nf.test.snap
+++ b/workflows/tests/aligner/bwa.nf.test.snap
@@ -221,7 +221,7 @@
"multiqc/multiqc_data/samtools_alignment_plot.txt",
"multiqc/multiqc_report.html",
"pipeline_info",
- "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+ "pipeline_info/nf_core_nascent_software_mqc_versions.yml",
"preprocessing",
"preprocessing/fastp",
"preprocessing/fastp/cd4_REP1.trimmed.fastp.html",
@@ -462,4 +462,4 @@
},
"timestamp": "2024-12-18T07:07:22.737667"
}
-}
\ No newline at end of file
+}
diff --git a/workflows/tests/aligner/bwamem2.nf.test b/workflows/tests/aligner/bwamem2.nf.test
index ae80dd8d..2bebf8ff 100644
--- a/workflows/tests/aligner/bwamem2.nf.test
+++ b/workflows/tests/aligner/bwamem2.nf.test
@@ -25,7 +25,7 @@ nextflow_pipeline {
// Number of tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
- removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+ removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml"),
// All stable path name
stable_name,
// All files with stable contents
diff --git a/workflows/tests/aligner/bwamem2.nf.test.snap b/workflows/tests/aligner/bwamem2.nf.test.snap
index be3f1f96..257d9d93 100644
--- a/workflows/tests/aligner/bwamem2.nf.test.snap
+++ b/workflows/tests/aligner/bwamem2.nf.test.snap
@@ -186,7 +186,7 @@
"multiqc/multiqc_data/samtools_alignment_plot.txt",
"multiqc/multiqc_report.html",
"pipeline_info",
- "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+ "pipeline_info/nf_core_nascent_software_mqc_versions.yml",
"preprocessing",
"preprocessing/fastp",
"preprocessing/fastp/cd4_REP1.trimmed.fastp.html",
diff --git a/workflows/tests/aligner/hisat2.nf.test b/workflows/tests/aligner/hisat2.nf.test
index fc030f6e..8deb6f2b 100644
--- a/workflows/tests/aligner/hisat2.nf.test
+++ b/workflows/tests/aligner/hisat2.nf.test
@@ -28,7 +28,7 @@ nextflow_pipeline {
// Number of tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
- removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+ removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml"),
// All stable path name
stable_name,
// All files with stable contents
diff --git a/workflows/tests/aligner/hisat2.nf.test.snap b/workflows/tests/aligner/hisat2.nf.test.snap
index 7296f90b..815b8f9a 100644
--- a/workflows/tests/aligner/hisat2.nf.test.snap
+++ b/workflows/tests/aligner/hisat2.nf.test.snap
@@ -187,7 +187,7 @@
"multiqc/multiqc_data/samtools_alignment_plot.txt",
"multiqc/multiqc_report.html",
"pipeline_info",
- "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+ "pipeline_info/nf_core_nascent_software_mqc_versions.yml",
"preprocessing",
"preprocessing/fastp",
"preprocessing/fastp/cd4_REP1.trimmed.fastp.html",
diff --git a/workflows/tests/aligner/star.nf.test b/workflows/tests/aligner/star.nf.test
index 34db1e0a..1fbcd996 100644
--- a/workflows/tests/aligner/star.nf.test
+++ b/workflows/tests/aligner/star.nf.test
@@ -27,7 +27,7 @@ nextflow_pipeline {
// Number of tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
- removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+ removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml"),
// All stable path name
stable_name,
// All files with stable contents
@@ -52,7 +52,7 @@ nextflow_pipeline {
then {
assertAll(
{ assert workflow.success },
- { assert snapshot(removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml")).match("gzip_software_versions") },
+ { assert snapshot(removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml")).match("gzip_software_versions") },
{ assert snapshot(
workflow.trace.tasks().size(),
).match()
diff --git a/workflows/tests/aligner/star.nf.test.snap b/workflows/tests/aligner/star.nf.test.snap
index b1552de6..f19dd9c4 100644
--- a/workflows/tests/aligner/star.nf.test.snap
+++ b/workflows/tests/aligner/star.nf.test.snap
@@ -157,7 +157,7 @@
"multiqc/multiqc_data/samtools_alignment_plot.txt",
"multiqc/multiqc_report.html",
"pipeline_info",
- "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+ "pipeline_info/nf_core_nascent_software_mqc_versions.yml",
"preprocessing",
"preprocessing/fastp",
"preprocessing/fastp/cd4_REP1.trimmed.fastp.html",
@@ -475,4 +475,4 @@
},
"timestamp": "2024-11-25T21:02:16.63526"
}
-}
\ No newline at end of file
+}
diff --git a/workflows/tests/inputs/gff/main.nf.test b/workflows/tests/inputs/gff/main.nf.test
index 7bec5f64..258a30bf 100644
--- a/workflows/tests/inputs/gff/main.nf.test
+++ b/workflows/tests/inputs/gff/main.nf.test
@@ -27,7 +27,7 @@ nextflow_pipeline {
// Number of tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
- removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+ removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml"),
// All stable path name
stable_name,
// All files with stable contents
diff --git a/workflows/tests/inputs/gff/main.nf.test.snap b/workflows/tests/inputs/gff/main.nf.test.snap
index 0ffc76f9..1b41f1b6 100644
--- a/workflows/tests/inputs/gff/main.nf.test.snap
+++ b/workflows/tests/inputs/gff/main.nf.test.snap
@@ -171,7 +171,7 @@
"multiqc/multiqc_data/samtools_alignment_plot.txt",
"multiqc/multiqc_report.html",
"pipeline_info",
- "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+ "pipeline_info/nf_core_nascent_software_mqc_versions.yml",
"preprocessing",
"preprocessing/fastp",
"preprocessing/fastp/cd4_REP1.trimmed.fastp.html",
diff --git a/workflows/tests/inputs/gzipped_gff/main.nf.test b/workflows/tests/inputs/gzipped_gff/main.nf.test
index 0bf35086..33bc949f 100644
--- a/workflows/tests/inputs/gzipped_gff/main.nf.test
+++ b/workflows/tests/inputs/gzipped_gff/main.nf.test
@@ -27,7 +27,7 @@ nextflow_pipeline {
// Number of tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
- removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+ removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml"),
// All stable path name
stable_name,
// All files with stable contents
diff --git a/workflows/tests/inputs/gzipped_gff/main.nf.test.snap b/workflows/tests/inputs/gzipped_gff/main.nf.test.snap
index 4660736c..f376150c 100644
--- a/workflows/tests/inputs/gzipped_gff/main.nf.test.snap
+++ b/workflows/tests/inputs/gzipped_gff/main.nf.test.snap
@@ -171,7 +171,7 @@
"multiqc/multiqc_data/samtools_alignment_plot.txt",
"multiqc/multiqc_report.html",
"pipeline_info",
- "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+ "pipeline_info/nf_core_nascent_software_mqc_versions.yml",
"preprocessing",
"preprocessing/fastp",
"preprocessing/fastp/cd4_REP1.trimmed.fastp.html",
diff --git a/workflows/tests/inputs/only_gff/main.nf.test b/workflows/tests/inputs/only_gff/main.nf.test
index 74841c14..b9fd1389 100644
--- a/workflows/tests/inputs/only_gff/main.nf.test
+++ b/workflows/tests/inputs/only_gff/main.nf.test
@@ -29,7 +29,7 @@ nextflow_pipeline {
// Number of tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
- removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+ removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml"),
// All stable path name
stable_name,
// All files with stable contents
diff --git a/workflows/tests/inputs/only_gff/main.nf.test.snap b/workflows/tests/inputs/only_gff/main.nf.test.snap
index 77e4d408..c7fe6492 100644
--- a/workflows/tests/inputs/only_gff/main.nf.test.snap
+++ b/workflows/tests/inputs/only_gff/main.nf.test.snap
@@ -174,7 +174,7 @@
"multiqc/multiqc_data/samtools_alignment_plot.txt",
"multiqc/multiqc_report.html",
"pipeline_info",
- "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+ "pipeline_info/nf_core_nascent_software_mqc_versions.yml",
"preprocessing",
"preprocessing/fastp",
"preprocessing/fastp/cd4_REP1.trimmed.fastp.html",
diff --git a/workflows/tests/inputs/uniqmap/main.nf.test b/workflows/tests/inputs/uniqmap/main.nf.test
index 04db908c..945b0929 100644
--- a/workflows/tests/inputs/uniqmap/main.nf.test
+++ b/workflows/tests/inputs/uniqmap/main.nf.test
@@ -21,7 +21,7 @@ nextflow_pipeline {
then {
assertAll(
{ assert workflow.success },
- { assert snapshot(removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml")).match("software_versions") },
+ { assert snapshot(removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml")).match("software_versions") },
// Files should have -uniqmap in the header
{ assert path("$outputDir/transcript_identification/homer/cd4.bed").readLines()[18].contains("uniqMapDirectory = uniqmap.GRCh38_chr21.50nt") },
{ assert path("$outputDir/transcript_identification/homer/cd4.bed").readLines()[20].contains("-uniqmap") },
diff --git a/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test b/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test
index 57367003..638a7ba0 100644
--- a/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test
+++ b/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test
@@ -33,7 +33,7 @@ nextflow_pipeline {
// Number of tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
- removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+ removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml"),
// All stable path name
stable_name,
// All files with stable contents
diff --git a/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test.snap b/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test.snap
index 66d1544f..c394efd9 100644
--- a/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test.snap
+++ b/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test.snap
@@ -184,7 +184,7 @@
"multiqc/multiqc_data/samtools_alignment_plot.txt",
"multiqc/multiqc_report.html",
"pipeline_info",
- "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+ "pipeline_info/nf_core_nascent_software_mqc_versions.yml",
"preprocessing",
"preprocessing/fastp",
"preprocessing/fastp/cd4_REP1.trimmed.fastp.html",
@@ -383,4 +383,4 @@
},
"timestamp": "2024-12-18T08:07:15.190593"
}
-}
\ No newline at end of file
+}
diff --git a/workflows/tests/transcript_indentification/grohmm/tuning/main.nf.test b/workflows/tests/transcript_indentification/grohmm/tuning/main.nf.test
index a300f206..847b907c 100644
--- a/workflows/tests/transcript_indentification/grohmm/tuning/main.nf.test
+++ b/workflows/tests/transcript_indentification/grohmm/tuning/main.nf.test
@@ -25,7 +25,7 @@ nextflow_pipeline {
// Number of tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
- removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+ removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml"),
// All stable path name
stable_name,
// All files with stable contents
diff --git a/workflows/tests/transcript_indentification/grohmm/tuning/main.nf.test.snap b/workflows/tests/transcript_indentification/grohmm/tuning/main.nf.test.snap
index 093d9bbe..877e3f4d 100644
--- a/workflows/tests/transcript_indentification/grohmm/tuning/main.nf.test.snap
+++ b/workflows/tests/transcript_indentification/grohmm/tuning/main.nf.test.snap
@@ -175,7 +175,7 @@
"multiqc/multiqc_data/samtools_alignment_plot.txt",
"multiqc/multiqc_report.html",
"pipeline_info",
- "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+ "pipeline_info/nf_core_nascent_software_mqc_versions.yml",
"preprocessing",
"preprocessing/fastp",
"preprocessing/fastp/cd4_REP1.trimmed.fastp.html",
@@ -374,4 +374,4 @@
},
"timestamp": "2024-12-18T08:25:02.333169"
}
-}
\ No newline at end of file
+}