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Move parameters to configuration file, add run script #4

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cleaned up paths
erflynn committed Jun 7, 2022
commit 5ebb54fcf7a0885594d1c60ef6fa2e75a03b3875
29 changes: 15 additions & 14 deletions bulk_RNASeq/pipeline.nf
Original file line number Diff line number Diff line change
@@ -217,7 +217,7 @@ process transcriptomeBAMToCRAM {
publishDir "${params.outdir}/${sample}/alignments/", mode: 'copy', pattern: "${sample}.transcriptome.trimmed.star.cram"

container "${params.container.samtools}"
containerOptions "-B ${params.ref.rsem_star_transcript_ref_dir}"
containerOptions "-B ${params.ref.rsem_star_dir}"
cpus 16
memory '50G'

@@ -240,22 +240,22 @@ process transcriptomeBAMToCRAM {
samtools view -@ ${task.cpus} \
-C \
--no-PG \
-T ${params.ref.rsem_star_transcript_ref_dir}/${params.ref.rsem_star_transcript_ref_prefix}.transcripts.fa \
-T ${params.ref.rsem_star_dir}/${params.ref.genome_version}.transcripts.fa \
-o ${sample}.trimmed.star.Transcriptome.mapped.cram \
${sample}.trimmed.star.Transcriptome.mapped.bam
"""
}


/*
* Step 7b. Extract and convert mapped genome
* Step 7b. Extract mapped genome
*/
process extractMappedGenome {
tag { "${sample}--${params.cohort_name}" }


container "${params.container.samtools}"
containerOptions "-B ${params.ref.rsem_star_transcript_ref_dir}"

cpus 16
memory '50G'

@@ -317,7 +317,7 @@ process dedupGenomeBAMToCRAM {
publishDir "${params.outdir}/${sample}/alignments/", mode: 'copy', pattern: "${sample}.trimmed.star.Aligned.sortedByCoord.out.deduplicated.cram*"

container "${params.container.samtools}"
containerOptions "-B ${params.ref.sequence_ref_dir}"
containerOptions "-B ${params.dirs.genome}"
cpus 16
memory '50G'

@@ -338,7 +338,7 @@ process dedupGenomeBAMToCRAM {
--no-PG \
--write-index \
-C \
-T ${params.ref.sequence_ref_dir}/${params.ref.fasta_file} \
-T ${params.ref.genome_fasta_file} \
-o ${sample}.trimmed.star.Aligned.sortedByCoord.out.deduplicated.cram \
${dg_bam}
@@ -355,7 +355,7 @@ process runRSEM {
publishDir "${params.outdir}/${sample}/alignments/", mode: 'copy', pattern: "${sample}.rsem.*.results"

container "${params.container.rsem}"
containerOptions "-B ${params.ref.rsem_star_transcript_ref_dir}"
containerOptions "-B ${params.ref.rsem_star_dir}"
cpus 12
memory '50G'

@@ -372,7 +372,7 @@ process runRSEM {
--alignments \
--num-threads ${task.cpus} \
${t_bam} \
${params.ref.rsem_star_transcript_ref_dir}/${params.ref.rsem_star_transcript_ref_prefix} \
${params.ref.rsem_star_dir}/${params.ref.genome_version} \
${sample}.rsem
"""
}
@@ -416,7 +416,8 @@ process dedupGenomeBAMRSQMetrics {
publishDir "${params.outdir}/${sample}/alignments/", mode: 'copy', pattern: "${sample}.trimmed.star.Aligned.sortedByCoord.out.deduplicated.rnaseq_metrics"

container "${params.container.picard}"
containerOptions "-B ${params.ref.genome_flat_ref_dir} -B ${params.ref.ribosomal_intervals_dir}"
containerOptions "-B ${params.dirs.genome}"

cpus 12
memory '50G'

@@ -433,8 +434,8 @@ process dedupGenomeBAMRSQMetrics {
-VALIDATION_STRINGENCY SILENT \
-ASSUME_SORTED true \
-STRAND_SPECIFICITY NONE \
-REF_FLAT ${params.ref.genome_flat_ref_dir}/${params.ref.genome_flat_ref_filename} \
-RIBOSOMAL_INTERVALS ${params.ref.ribosomal_intervals_dir}/${params.ref.ribosomal_intervals_filename} \
-REF_FLAT ${params.ref.genome_flat_file} \
-RIBOSOMAL_INTERVALS ${params.ref.ribosomal_intervals_file} \
-I ${dg_bam} \
-OUTPUT ${sample}.trimmed.star.Aligned.sortedByCoord.out.deduplicated.rnaseq_metrics
"""
@@ -523,7 +524,7 @@ process splitBAM {

"""
gatk SplitNCigarReads \
-R ${params.ref.sequence_ref_dir}/${params.ref.fasta_file} \
-R ${params.ref.genome_fasta_file} \
-I ${rg_bam} \
-O ${sample}.withRG.nSplit.bam
@@ -550,7 +551,7 @@ process runGATK {
"""
gatk HaplotypeCaller \
-L ${params.ref.exon_bed} \
-R ${params.ref.sequence_ref_dir}/${params.ref.fasta_file} \
-R ${params.ref.genome_fasta_file} \
-D ${params.ref.dbsnp} \
-I ${split_bam} \
--dont-use-soft-clipped-bases true -stand-call-conf 20.0 \
@@ -580,7 +581,7 @@ process filterGATK {
"""
gatk VariantFiltration \
-L ${params.ref.exon_bed} \
-R ${params.ref.sequence_ref_dir}/${params.ref.fasta_file} \
-R ${params.ref.genome_fasta_file} \
-V ${raw_gatk} \
-window 35 -cluster 3 \
--filter-name FS -filter "FS > 30.0" \
16 changes: 6 additions & 10 deletions bulk_RNASeq/tool.config
Original file line number Diff line number Diff line change
@@ -15,19 +15,15 @@ params {
genome_version = 'hg38'
adapter_seq1 = 'CTGTCTCTTATACACATCT'
adapter_seq2 = 'CTGTCTCTTATACACATCT'
rsem_star_transcript_ref_dir = "${params.dirs.genome}/rsem_all/"
rsem_star_transcript_ref_prefix = "hg38"
rsem_star_dir = "${params.dirs.genome}/rsem/"
dbsnp = "${params.dirs.genome}/GCF_000001405.39_mapped.txt.gz"
exon_bed = "${params.dirs.genome}/exon_only.bed"
genome_flat_ref_dir = "${params.dirs.genome}"
genome_flat_ref_filename = "gencode.v38.chr_patch_hapl_scaff.annotation_flat.txt"
genome_flat_file = "${params.dirs.genome}/gencode.v38.chr_patch_hapl_scaff.annotation_flat.txt"
gtf_ref = "${params.dirs.genome}/gencode.v38.chr_patch_hapl_scaff.annotation.gtf"
ribosomal_intervals_dir = "${params.dirs.genome}"
ribosomal_intervals_filename = "ribo_intervals_all.txt"
star_genome_dir = "${params.dirs.genome}/star_all/"
sequence_ref_dir = "${params.dirs.genome}"
fasta_file = "GRCh38.p13.genome.fa"
kallisto_dir = "${params.dirs.genome}/kallisto_all/"
ribosomal_intervals_file = "${params.dirs.genome}/ribo_intervals.txt"
star_genome_dir = "${params.dirs.genome}/star/"
genome_fasta_file = "${params.dirs.genome}/GRCh38.p13.genome.fa"
kallisto_dir = "${params.dirs.genome}/kallisto/"
kallisto_index = "GRCh38.p13.index"
}
}