Fix linting

.github/workflows/branch.yml

@@ -9,8 +9,7 @@ jobs:
   test:
     runs-on: ubuntu-18.04
     steps:
-      # PRs are only ok if coming from an nf-core dev branch
-      - uses: actions/checkout@v1
+      # PRs are only ok if coming from an nf-core `dev` branch or a fork `patch` branch
       - name: Check PRs
         run: |
           { [[ $(git remote get-url origin) == *nf-core/sarek ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; } || [[ ${GITHUB_HEAD_REF} == "patch" ]]

.github/workflows/ci.yml

@@ -17,17 +17,16 @@ jobs:
           sudo mv nextflow /usr/local/bin/
       - name: Download and tag image
         run: |
-          docker pull nfcore/sarek:dev
-          docker tag nfcore/sarek:dev nfcore/sarek:dev
+          docker pull nfcore/sarek:dev && docker tag nfcore/sarek:dev nfcore/sarek:dev
       - name: Run test
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker
   annotation:
     runs-on: ubuntu-18.04
     strategy:
       matrix:
-        annotator: [snpeff]
-        specie: [GRCh37]
+        tools: [snpeff]
+        species: [GRCh37]
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow
@@ -38,13 +37,12 @@ jobs:
           NXF_VER: '19.10.0'
       - name: Download and tag images
         run: |
-          docker pull nfcore/sarek:dev
-          docker tag nfcore/sarek:dev nfcore/sarek:dev
-          docker pull nfcore/sarek${{ matrix.annotator }}:dev.${{ matrix.specie }}
-          docker tag nfcore/sarek${{ matrix.annotator }}:dev.${{ matrix.specie }} nfcore/sarek${{ matrix.annotator }}:dev.${{ matrix.specie }}
+          docker pull nfcore/sarek:dev && docker tag nfcore/sarek:dev nfcore/sarek:dev
+          docker pull nfcore/sarek${{ matrix.tools }}:dev.${{ matrix.species }}
+          docker tag nfcore/sarek${{ matrix.tools }}:dev.${{ matrix.species }} nfcore/sarek${{ matrix.tools }}:dev.${{ matrix.species }}
       - name: Run annotation test
         run: |
-          nextflow run . -profile test_annotation,docker --verbose --tools ${{ matrix.annotator }}
+          nextflow run . -profile test_annotation,docker --verbose --tools ${{ matrix.tools }}
   germline:
     runs-on: ubuntu-18.04
     steps:
@@ -57,8 +55,7 @@ jobs:
           NXF_VER: '19.10.0'
       - name: Download and tag image
         run: |
-          docker pull nfcore/sarek:dev
-          docker tag nfcore/sarek:dev nfcore/sarek:dev
+          docker pull nfcore/sarek:dev && docker tag nfcore/sarek:dev nfcore/sarek:dev
       - name: Get test data
         run: |
           git clone --single-branch --branch sarek https://github.com/nf-core/test-datasets.git data
@@ -83,8 +80,7 @@ jobs:
           NXF_VER: '19.10.0'
       - name: Download and tag image
         run: |
-          docker pull nfcore/sarek:dev
-          docker tag nfcore/sarek:dev nfcore/sarek:dev
+          docker pull nfcore/sarek:dev && docker tag nfcore/sarek:dev nfcore/sarek:dev
       - name: Run test for minimal genomes
         run: |
           nextflow run . -profile test,docker --skipQC all --verbose --genome ${{ matrix.genome }} ${{ matrix.intervals }} --tools Manta,mpileup,Strelka
@@ -103,8 +99,7 @@ jobs:
           NXF_VER: '19.10.0'
       - name: Download and tag image
         run: |
-          docker pull nfcore/sarek:dev
-          docker tag nfcore/sarek:dev nfcore/sarek:dev
+          docker pull nfcore/sarek:dev && docker tag nfcore/sarek:dev nfcore/sarek:dev
       - name: Run ${{ matrix.profile }} test
         run: |
           nextflow run . -profile ${{ matrix.profile }},docker --verbose
@@ -123,8 +118,7 @@ jobs:
           NXF_VER: '19.10.0'
       - name: Download and tag image
         run: |
-          docker pull nfcore/sarek:dev
-          docker tag nfcore/sarek:dev nfcore/sarek:dev
+          docker pull nfcore/sarek:dev && docker tag nfcore/sarek:dev nfcore/sarek:dev
       - name: Run ${{ matrix.tool }} test
         run: |
           nextflow run . -profile test_tool,docker --verbose --tools ${{ matrix.tool }}

.github/workflows/linting.yml

@@ -47,7 +47,7 @@ jobs:
           pip install --upgrade pip
       - name: Install nf-core tools
         run: |
-          pip install nf-core
+          pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
       - name: Run nf-core lint
         run: |
           nf-core lint ${GITHUB_WORKSPACE}

CHANGELOG.md

@@ -17,10 +17,50 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 - [#76](https://github.com/nf-core/sarek/pull/76) - Use `gatk4-spark` instead of `gatk4` in `environment.yml`
 - [#80](https://github.com/nf-core/sarek/pull/80) - Re-bump `dev` branch
 - [#85](https://github.com/nf-core/sarek/pull/85) - Use new merged vcf files for known indels to simplify setting up channel
+- [#107](https://github.com/nf-core/sarek/pull/107) - Switch params to snake_case
 
 ### `Fixed`
 
 - [#83](https://github.com/nf-core/sarek/pull/83) - Fix some typos in `docs/input.md`
+- [#107](https://github.com/nf-core/sarek/pull/107) - Fix linting
+
+### `Deprecated`
+
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--annotateTools` is now deprecated, use `--annotate_tools` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--cadd_InDels` is now deprecated, use `--cadd_indels` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--cadd_InDels_tbi` is now deprecated, use `--cadd_indels_tbi` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--cadd_WG_SNVs` is now deprecated, use `--cadd_wg_snvs` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--cadd_WG_SNVs_tbi` is now deprecated, use `--cadd_wg_snvs_tbi` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--maxMultiqcEmailFileSize` is now deprecated, use `--max_multiqc_email_size` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--noGVCF` is now deprecated, use `--no_gvcf` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--noStrelkaBP` is now deprecated, use `--no_strelka_bp` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--nucleotidesPerSecond` is now deprecated, use `--nucleotides_per_second` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--publishDirMode` is now deprecated, use `--publish_dir_mode` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--saveGenomeIndex` is now deprecated, use `--save_reference` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--skipQC` is now deprecated, use `--skip_qc` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--snpEff_cache` is now deprecated, use `--snpeff_cache` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--targetBed` is now deprecated, use `--target_bed` instead
+
+### `Removed`
+
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--acLociGC` is now removed, use `--ac_loci_gc` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--acLoci` is now removed, use `--ac_loci` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--bwaIndex` is now removed, use `--bwa` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--chrDir` is now removed, use `--chr_dir` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--chrLength` is now removed, use `--chr_length` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--dbsnpIndex` is now removed, use `--dbsnp_index` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--fastaFai` is now removed, use `--fasta_fai` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--genomeDict` is now removed, use `--dict` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--genomeFile` is now removed, use `--fasta` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--genomeIndex` is now removed, use `--fasta_fai` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--germlineResourceIndex` is now removed, use `--germline_resource_index` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--germlineResource` is now removed, use `--germline_resource` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--igenomesIgnore` is now removed, use `--igenomes_ignore` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--knownIndelsIndex` is now removed, use `--known_indels_index` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--knownIndels` is now removed, use `--known_indels` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--singleCPUMem` is now removed, use `--single_cpu_mem` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--snpeffDb` is now removed, use `--snpeff_db` instead
+- [#107](https://github.com/nf-core/sarek/pull/107) - `--vepCacheVersion` is now removed, use `--vep_cache_version` instead
 
 ## [2.5.2] - Jåkkåtjkaskajekna
 

Dockerfile

@@ -1,7 +1,8 @@
-FROM nfcore/base:1.7
+FROM nfcore/base:dev
 LABEL authors="Maxime Garcia, Szilveszter Juhos" \
       description="Docker image containing all requirements for nf-core/sarek pipeline"
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-sarek-dev/bin:$PATH
+RUN conda env export --name nf-core-sarek-dev > nf-core-sarek-dev.yml
+ENV PATH /opt/conda/envs/nf-core-sarek-dev/bin:$PATH

conf/base.config

@@ -11,7 +11,7 @@
 
 process {
   cpus = {check_resource(params.cpus * task.attempt)}
-  memory = {check_resource((params.singleCPUMem as nextflow.util.MemoryUnit) * task.attempt)}
+  memory = {check_resource((params.single_cpu_mem as nextflow.util.MemoryUnit) * task.attempt)}
   time = {check_resource(24.h * task.attempt)}
   shell = ['/bin/bash', '-euo', 'pipefail']
 
@@ -39,10 +39,10 @@ process {
   }
 
   withLabel:memory_singleCPU_2_task {
-    memory = {check_resource((params.singleCPUMem as nextflow.util.MemoryUnit) * 2 * task.attempt)}
+    memory = {check_resource((params.single_cpu_mem as nextflow.util.MemoryUnit) * 2 * task.attempt)}
   }
   withLabel:memory_singleCPU_task_sq {
-    memory = {check_resource((params.singleCPUMem as nextflow.util.MemoryUnit) * task.attempt * task.attempt)}
+    memory = {check_resource((params.single_cpu_mem as nextflow.util.MemoryUnit) * task.attempt * task.attempt)}
   }
 
   withLabel:memory_max {

conf/genomes.config

@@ -10,61 +10,61 @@
 params {
   genomes {
     'GRCh37' {
-      acLoci                = "${params.genomes_base}/1000G_phase3_20130502_SNP_maf0.3.loci"
-      acLociGC              = "${params.genomes_base}/1000G_phase3_20130502_SNP_maf0.3.loci.gc"
-      bwaIndex              = "${params.genomes_base}/human_g1k_v37_decoy.fasta.{amb,ann,bwt,pac,sa}"
-      chrDir                = "${params.genomes_base}/Chromosomes"
-      chrLength             = "${params.genomes_base}/human_g1k_v37_decoy.len"
-      dbsnp                 = "${params.genomes_base}/dbsnp_138.b37.vcf"
-      dbsnpIndex            = "${params.genomes_base}/dbsnp_138.b37.vcf.idx"
-      dict                  = "${params.genomes_base}/human_g1k_v37_decoy.dict"
-      fasta                 = "${params.genomes_base}/human_g1k_v37_decoy.fasta"
-      fastaFai              = "${params.genomes_base}/human_g1k_v37_decoy.fasta.fai"
-      germlineResource      = "${params.genomes_base}/gnomAD.r2.1.1.GRCh37.PASS.AC.AF.only.vcf.gz"
-      germlineResourceIndex = "${params.genomes_base}/gnomAD.r2.1.1.GRCh37.PASS.AC.AF.only.vcf.gz.tbi"
-      intervals             = "${params.genomes_base}/wgs_calling_regions_Sarek.list"
-      knownIndels           = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf"
-      knownIndelsIndex      = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
-      snpeffDb              = 'GRCh37.75'
-      species               = 'homo_sapiens'
-      vepCacheVersion       = '95'
+      ac_loci                 = "${params.genomes_base}/1000G_phase3_20130502_SNP_maf0.3.loci"
+      ac_loci_gc              = "${params.genomes_base}/1000G_phase3_20130502_SNP_maf0.3.loci.gc"
+      bwa                     = "${params.genomes_base}/human_g1k_v37_decoy.fasta.{amb,ann,bwt,pac,sa}"
+      chr_dir                 = "${params.genomes_base}/Chromosomes"
+      chr_length              = "${params.genomes_base}/human_g1k_v37_decoy.len"
+      dbsnp                   = "${params.genomes_base}/dbsnp_138.b37.vcf"
+      dbsnp_index             = "${params.genomes_base}/dbsnp_138.b37.vcf.idx"
+      dict                    = "${params.genomes_base}/human_g1k_v37_decoy.dict"
+      fasta                   = "${params.genomes_base}/human_g1k_v37_decoy.fasta"
+      fasta_fai               = "${params.genomes_base}/human_g1k_v37_decoy.fasta.fai"
+      germline_resource       = "${params.genomes_base}/gnomAD.r2.1.1.GRCh37.PASS.AC.AF.only.vcf.gz"
+      germline_resource_index = "${params.genomes_base}/gnomAD.r2.1.1.GRCh37.PASS.AC.AF.only.vcf.gz.tbi"
+      intervals               = "${params.genomes_base}/wgs_calling_regions_Sarek.list"
+      known_indels            = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf"
+      known_indels_index      = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
+      snpeff_db               = 'GRCh37.75'
+      species                 = 'homo_sapiens'
+      vep_cache_version       = '95'
     }
     'GRCh38' {
-      acLoci                = "${params.genomes_base}/1000G_phase3_GRCh38_maf0.3.loci"
-      acLociGC              = "${params.genomes_base}/1000G_phase3_GRCh38_maf0.3.loci.gc"
-      bwaIndex              = "${params.genomes_base}/Homo_sapiens_assembly38.fasta.64.{alt,amb,ann,bwt,pac,sa}"
-      chrDir                = "${params.genomes_base}/Chromosomes"
-      chrLength             = "${params.genomes_base}/Homo_sapiens_assembly38.len"
-      dbsnp                 = "${params.genomes_base}/dbsnp_146.hg38.vcf.gz"
-      dbsnpIndex            = "${params.genomes_base}/dbsnp_146.hg38.vcf.gz.tbi"
-      dict                  = "${params.genomes_base}/Homo_sapiens_assembly38.dict"
-      fasta                 = "${params.genomes_base}/Homo_sapiens_assembly38.fasta"
-      fastaFai              = "${params.genomes_base}/Homo_sapiens_assembly38.fasta.fai"
-      germlineResource      = "${params.genomes_base}/gnomAD.r2.1.1.GRCh38.PASS.AC.AF.only.vcf.gz"
-      germlineResourceIndex = "${params.genomes_base}/gnomAD.r2.1.1.GRCh38.PASS.AC.AF.only.vcf.gz.tbi"
-      intervals             = "${params.genomes_base}/wgs_calling_regions.hg38.bed"
-      knownIndels           = "${params.genomes_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
-      knownIndelsIndex      = "${params.genomes_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
-      snpeffDb              = 'GRCh38.86'
-      species               = 'homo_sapiens'
-      vepCacheVersion       = '95'
+      ac_loci                 = "${params.genomes_base}/1000G_phase3_GRCh38_maf0.3.loci"
+      ac_loci_gc              = "${params.genomes_base}/1000G_phase3_GRCh38_maf0.3.loci.gc"
+      bwa                     = "${params.genomes_base}/Homo_sapiens_assembly38.fasta.64.{alt,amb,ann,bwt,pac,sa}"
+      chr_dir                 = "${params.genomes_base}/Chromosomes"
+      chr_length              = "${params.genomes_base}/Homo_sapiens_assembly38.len"
+      dbsnp                   = "${params.genomes_base}/dbsnp_146.hg38.vcf.gz"
+      dbsnp_index             = "${params.genomes_base}/dbsnp_146.hg38.vcf.gz.tbi"
+      dict                    = "${params.genomes_base}/Homo_sapiens_assembly38.dict"
+      fasta                   = "${params.genomes_base}/Homo_sapiens_assembly38.fasta"
+      fasta_fai               = "${params.genomes_base}/Homo_sapiens_assembly38.fasta.fai"
+      germline_resource       = "${params.genomes_base}/gnomAD.r2.1.1.GRCh38.PASS.AC.AF.only.vcf.gz"
+      germline_resource_index = "${params.genomes_base}/gnomAD.r2.1.1.GRCh38.PASS.AC.AF.only.vcf.gz.tbi"
+      intervals               = "${params.genomes_base}/wgs_calling_regions.hg38.bed"
+      known_indels            = "${params.genomes_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
+      known_indels_index      = "${params.genomes_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
+      snpeff_db               = 'GRCh38.86'
+      species                 = 'homo_sapiens'
+      vep_cache_version       = '95'
     }
     'minimalGRCh37' {
-      fasta                 = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
+      fasta                   = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
     }
     'smallGRCh37' {
-      dbsnp                 = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz"
-      fasta                 = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
-      germlineResource      = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz"
-      intervals             = "${params.genomes_base}/small.intervals"
-      knownIndels           = "${params.genomes_base}/Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz"
-      snpeffDb              = 'GRCh37.75'
-      species               = 'homo_sapiens'
-      vepCacheVersion       = '95'
+      dbsnp                   = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz"
+      fasta                   = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
+      germline_resource       = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz"
+      intervals               = "${params.genomes_base}/small.intervals"
+      known_indels            = "${params.genomes_base}/Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz"
+      snpeff_db               = 'GRCh37.75'
+      species                 = 'homo_sapiens'
+      vep_cache_version       = '95'
     }
     'smallerGRCh37' {
-      fasta                 = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
-      knownIndels           = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz"
+      fasta                   = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
+      known_indels            = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz"
     }
   }
 }