Fix issus due to merging with TEMPLATE

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,6 +1,13 @@
-<!--
-# nf-core/sarek bug report
+---
+name: nf-core/sarek Bug report
+about: Create a report to help us improve
+title: "[BUG]"
+labels: bug
+assignees: MaxUlysse
+
+---
 
+<!--
 Hi there!
 
 Thanks for telling us about a problem with the pipeline.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,6 +1,13 @@
-<!--
-# nf-core/sarek feature request
+---
+name: nf-core/sarek Feature request
+about: Create a report to help us improve
+title: "[FEATURE]"
+labels: enhancement
+assignees: MaxUlysse
+
+---
 
+<!--
 Hi there!
 
 Thanks for suggesting a new feature for the pipeline!

.github/workflows/ci.yml

@@ -24,18 +24,15 @@ jobs:
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
-
       - name: Check if Dockerfile or Conda environment changed
         uses: technote-space/get-diff-action@v1
         with:
           PREFIX_FILTER: |
             Dockerfile
             environment.yml
-
       - name: Build new docker image
         if: env.GIT_DIFF
         run: docker build --no-cache . -t nfcore/sarek:dev
-
       - name: Pull docker image
         if: ${{ !env.GIT_DIFF }}
         run: |
@@ -59,6 +56,10 @@ jobs:
         species: [WBcel235]
     steps:
       - uses: actions/checkout@v2
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
         env:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '19.10.0'

README.md

@@ -42,8 +42,8 @@ It's listed on [Elixir - Tools and Data Services Registry](https://bio.tools/Sar
     ```
 
     > Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute.
-    If so, you can simply use `-profile <institute>` in your command.
-    This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
+    > If so, you can simply use `-profile <institute>` in your command.
+    > This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
 
 4. Start running your own analysis!
 

bin/scrape_software_versions.py

@@ -15,7 +15,7 @@
     "GATK": ["v_gatk.txt", r"Version:(\S+)"],
     "htslib": ["v_samtools.txt", r"htslib (\S+)"],
     "Manta": ["v_manta.txt", r"([0-9.]+)"],
-    "msisensor': ["v_msisensor.txt", r"Version: v(\S+)"],
+    "msisensor": ["v_msisensor.txt", r"Version: v(\S+)"],
     "MultiQC": ["v_multiqc.txt", r"multiqc, version (\S+)"],
     "Nextflow": ["v_nextflow.txt", r"(\S+)"],
     "nf-core/sarek": ["v_pipeline.txt", r"(\S+)"],

docs/output.md

@@ -5,6 +5,7 @@ This document describes the output produced by the pipeline.
 The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.
 
 ## Pipeline overview <!-- omit in toc -->
+
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
 - [Preprocessing](#preprocessing)

main.nf

@@ -182,196 +182,6 @@ def helpMessage() {
 // Show help message
 if (params.help) exit 0, helpMessage()
 
-/*
-================================================================================
-                                HANDLE OLD PARAMS
-================================================================================
-*/
-
-// Warnings for deprecated params
-
-params.annotateTools = null
-if (params.annotateTools) {
-    log.warn "The params `--annotateTools` is deprecated -- it will be removed in a future release."
-    log.warn "\tPlease check: https://nf-co.re/sarek/docs/usage.md#--annotate_tools"
-    params.annotate_tools = params.annotateTools
-}
-
-params.annotateVCF = null
-if (params.annotateVCF) {
-    log.warn "The params `--annotateVCF` is deprecated -- it will be removed in a future release."
-    log.warn "\tPlease check: https://nf-co.re/sarek/docs/usage.md#--input"
-    input = params.annotateVCF
-}
-
-params.cadd_InDels = null
-if (params.cadd_InDels) {
-    log.warn "The params `--cadd_InDels is deprecated -- it will be removed in a future release."
-    log.warn "\tPlease check: https://nf-co.re/sarek/docs/usage.md#--cadd_indels"
-    params.cadd_indels = params.cadd_InDels
-}
-
-params.cadd_InDels_tbi = null
-if (params.cadd_InDels_tbi) {
-    log.warn "The params `--cadd_InDels_tbi is deprecated -- it will be removed in a future release."
-    log.warn "\tPlease check: https://nf-co.re/sarek/docs/usage.md#--cadd_indels_tbi"
-    params.cadd_indels_tbi = params.cadd_InDels_tbi
-}
-
-params.cadd_WG_SNVs = null
-if (params.cadd_WG_SNVs) {
-    log.warn "The params `--cadd_WG_SNVs is deprecated -- it will be removed in a future release."
-    log.warn "\tPlease check: https://nf-co.re/sarek/docs/usage.md#--cadd_wg_snvs"
-    params.cadd_wg_snvs = params.cadd_WG_SNVs
-}
-
-params.cadd_WG_SNVs_tbi = null
-if (params.cadd_WG_SNVs_tbi) {
-    log.warn "The params `--cadd_WG_SNVs_tbi is deprecated -- it will be removed in a future release."
-    log.warn "\tPlease check: https://nf-co.re/sarek/docs/usage.md#--cadd_wg_snvs_tbi"
-    params.cadd_wg_snvs_tbi = params.cadd_WG_SNVs_tbi
-}
-
-params.maxMultiqcEmailFileSize = null
-if (params.maxMultiqcEmailFileSize) {
-    log.warn "The params `--maxMultiqcEmailFileSize` is deprecated -- it will be removed in a future release."
-    log.warn "\tPlease check: https://nf-co.re/sarek/docs/usage.md#--max_multiqc_email_size"
-    params.max_multiqc_email_size = params.maxMultiqcEmailFileSize
-}
-
-params.noGVCF = null
-if (params.noGVCF) {
-    log.warn "The params `--noGVCF` is deprecated -- it will be removed in a future release."
-    log.warn "\tPlease check: https://nf-co.re/sarek/docs/usage.md#--no_gvcf"
-    params.no_gvcf = params.noGVCF
-}
-
-params.noReports = null
-if (params.noReports) {
-    log.warn "The params `--noReports` is deprecated -- it will be removed in a future release."
-    log.warn "\tPlease check: https://nf-co.re/sarek/docs/usage.md#--skip_qc"
-    params.skip_qc = 'all'
-}
-
-params.noStrelkaBP = null
-if (params.noStrelkaBP) {
-    log.warn "The params `--noStrelkaBP` is deprecated -- it will be removed in a future release."
-    log.warn "\tPlease check: https://nf-co.re/sarek/docs/usage.md#--no_strelka_bp"
-    params.no_strelka_bp = params.noStrelkaBP
-}
-
-params.nucleotidesPerSecond = null
-if (params.nucleotidesPerSecond) {
-    log.warn "The params `--nucleotidesPerSecond` is deprecated -- it will be removed in a future release."
-    log.warn "\tPlease check: https://nf-co.re/sarek/docs/usage.md#--nucleotides_per_second"
-    params.nucleotides_per_second = params.nucleotidesPerSecond
-}
-
-params.publishDirMode = null
-if (params.publishDirMode) {
-    log.warn "The params `--publishDirMode` is deprecated -- it will be removed in a future release."
-    log.warn "\tPlease check: https://nf-co.re/sarek/docs/usage.md#--publish_dir_mode"
-    params.publish_dir_mode = params.publishDirMode
-}
-
-params.sample = null
-if (params.sample) {
-    log.warn "The params `--sample` is deprecated -- it will be removed in a future release."
-    log.warn "\tPlease check: https://nf-co.re/sarek/docs/usage.md#--input"
-    params.input = params.sample
-}
-
-params.sampleDir = null
-if (params.sampleDir) {
-    log.warn "The params `--sampleDir` is deprecated -- it will be removed in a future release."
-    log.warn "\tPlease check: https://nf-co.re/sarek/docs/usage.md#--input"
-    params.input = params.sampleDir
-}
-
-params.saveGenomeIndex = null
-if (params.saveGenomeIndex) {
-    log.warn "The params `--saveGenomeIndex` is deprecated -- it will be removed in a future release."
-    log.warn "\tPlease check: https://nf-co.re/sarek/docs/usage.md#--save_reference"
-    params.save_reference = params.saveGenomeIndex
-}
-
-params.skipQC = null
-if (params.skipQC) {
-    log.warn "The params `--skipQC` is deprecated -- it will be removed in a future release."
-    log.warn "\tPlease check: https://nf-co.re/sarek/docs/usage.md#--skip_qc"
-    params.skip_qc = params.skipQC
-}
-
-params.snpEff_cache = null
-if (params.snpEff_cache) {
-    log.warn "The params `--snpEff_cache` is deprecated -- it will be removed in a future release."
-    log.warn "\tPlease check: https://nf-co.re/sarek/docs/usage.md#--snpeff_cache"
-    params.snpeff_cache = params.snpEff_cache
-}
-
-params.targetBed = null
-if (params.targetBed) {
-    log.warn "The params `--targetBed` is deprecated -- it will be removed in a future release."
-    log.warn "\tPlease check: https://nf-co.re/sarek/docs/usage.md#--target_bed"
-    params.target_bed = params.targetBed
-}
-
-// Errors for removed params
-
-params.acLoci = null
-if (params.acLoci) exit 1, "The params `--acLoci` has been removed.\n\tPlease check: https://nf-co.re/sarek/docs/usage.md#--ac_loci"
-
-params.acLociGC = null
-if (params.acLociGC) exit 1, "The params `--acLociGC` has been removed.\n\tPlease check: https://nf-co.re/sarek/docs/usage.md#--ac_loci_gc"
-
-params.bwaIndex = null
-if (params.bwaIndex) exit 1, "The params `--bwaIndex` has been removed.\n\tPlease check: https://nf-co.re/sarek/docs/usage.md#--bwa"
-
-params.chrDir = null
-if (params.chrDir) exit 1, "The params `--chrDir` has been removed.\n\tPlease check: https://nf-co.re/sarek/docs/usage.md#--chr_dir"
-
-params.chrLength = null
-if (params.chrLength) exit 1, "The params `--chrLength` has been removed.\n\tPlease check: https://nf-co.re/sarek/docs/usage.md#--chr_length"
-
-params.dbsnpIndex = null
-if (params.dbsnpIndex) exit 1, "The params `--dbsnpIndex` has been removed.\n\tPlease check: https://nf-co.re/sarek/docs/usage.md#--dbsnp_index"
-
-params.fastaFai = null
-if (params.fastaFai) exit 1, "The params `--fastaFai` has been removed.\n\tPlease check: https://nf-co.re/sarek/docs/usage.md#--fasta_fai"
-
-params.genomeDict = null
-if (params.genomeDict) exit 1, "The params `--genomeDict` has been removed.\n\tPlease check: https://nf-co.re/sarek/docs/usage.md#--dict"
-
-params.genomeFile = null
-if (params.genomeFile) exit 1, "The params `--genomeFile` has been removed.\n\tPlease check: https://nf-co.re/sarek/docs/usage.md#--fasta"
-
-params.genomeIndex = null
-if (params.genomeIndex) exit 1, "The params `--genomeIndex` has been removed.\n\tPlease check: https://nf-co.re/sarek/docs/usage.md#--fasta_fai"
-
-params.germlineResource = null
-if (params.germlineResource) exit 1, "The params `--germlineResource` has been removed.\n\tPlease check: https://nf-co.re/sarek/docs/usage.md#--germline_resource"
-
-params.germlineResourceIndex = null
-if (params.germlineResourceIndex) exit 1, "The params `--germlineResourceIndex` has been removed.\n\tPlease check: https://nf-co.re/sarek/docs/usage.md#--germline_resource_index"
-
-params.igenomesIgnore = null
-if (params.igenomesIgnore) exit 1, "The params `--igenomesIgnore` has been removed.\n\tPlease check: https://nf-co.re/sarek/docs/usage.md#--igenomes_ignore"
-
-params.knownIndels = null
-if (params.knownIndels) exit 1, "The params `--knownIndels` has been removed.\n\tPlease check: https://nf-co.re/sarek/docs/usage.md#--known_indels"
-
-params.knownIndelsIndex = null
-if (params.knownIndelsIndex) exit 1, "The params `--knownIndelsIndex` has been removed.\n\tPlease check: https://nf-co.re/sarek/docs/usage.md#--known_indels_index"
-
-params.snpeffDb = null
-if (params.snpeffDb) exit 1, "The params `--snpeffDb` has been removed.\n\tPlease check: https://nf-co.re/sarek/docs/usage.md#--snpeff_db"
-
-params.singleCPUMem = null
-if (params.singleCPUMem) exit 1, "The params `--singleCPUMem` has been removed.\n\tPlease check: https://nf-co.re/sarek/docs/usage.md#--single_cpu_mem"
-
-params.vepCacheVersion = null
-if (params.vepCacheVersion) exit 1, "The params `--vepCacheVersion` has been removed.\n\tPlease check: https://nf-co.re/sarek/docs/usage.md#--vep_cache_version"
-
 /*
 ================================================================================
                          SET UP CONFIGURATION VARIABLES
@@ -432,6 +242,7 @@ if (workflow.profile.contains('awsbatch')) {
 ch_multiqc_config = file("$baseDir/assets/multiqc_config.yaml", checkIfExists: true)
 ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
 ch_output_docs = file("$baseDir/docs/output.md", checkIfExists: true)
+ch_output_docs_images = file("$baseDir/docs/images/", checkIfExists: true)
 
 // Handle input
 tsvPath = null
@@ -1205,7 +1016,7 @@ process TrimGalore {
 
 process UMIFastqToBAM {
 
-  publishDir "${params.outdir}/Reports/${idSample}/UMI/${idSample}_${idRun}", mode: params.publishDirMode
+  publishDir "${params.outdir}/Reports/${idSample}/UMI/${idSample}_${idRun}", mode: params.publish_dir_mode
 
   input:
     set idPatient, idSample, idRun, file("${idSample}_${idRun}_R1.fastq.gz"), file("${idSample}_${idRun}_R2.fastq.gz") from inputPairReadsUMI
@@ -1269,7 +1080,7 @@ process UMIMapBamFile {
 
 process GroupReadsByUmi {
 
-  publishDir "${params.outdir}/Reports/${idSample}/UMI/${idSample}_${idRun}", mode: params.publishDirMode
+  publishDir "${params.outdir}/Reports/${idSample}/UMI/${idSample}_${idRun}", mode: params.publish_dir_mode
 
   input:
       set idPatient, idSample, idRun, file(alignedBam) from umi_aligned_bams_ch
@@ -1305,7 +1116,7 @@ process GroupReadsByUmi {
 
 process CallMolecularConsensusReads {
 
-  publishDir "${params.outdir}/Reports/${idSample}/UMI/${idSample}_${idRun}", mode: params.publishDirMode
+  publishDir "${params.outdir}/Reports/${idSample}/UMI/${idSample}_${idRun}", mode: params.publish_dir_mode
 
   input:
       set idPatient, idSample, idRun, file(groupedBamFile) from umi_grouped_bams_ch

nextflow.config

@@ -37,7 +37,6 @@ params {
   three_prime_clip_r2 = 0
   trim_nextseq = 0
   save_trimmed = false
-  single_end = false // No single end
   split_fastq = null // Fastq files will not be split by default
 
   // Preprocessing