no more profile-ception

CHANGELOG.md

@@ -44,6 +44,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#728](https://github.com/nf-core/sarek/pull/728) - Circumvent issue with controlfreec and length file containing regions not in intervals file
 - [#729](https://github.com/nf-core/sarek/pull/729) - Trailing commas in `--tools`, `--skip_tools` and `--use_gatk_spark` now raise failure cf [#722](https://github.com/nf-core/sarek/issues/722)
 - [#741](https://github.com/nf-core/sarek/pull/741) - Fix prefix for `bcftools sort` for joint germline variant calling
+- [#743](https://github.com/nf-core/sarek/pull/743) - Remove profile definitions in profile to avoid issues with Tower
 
 ### Deprecated
 

conf/base.config

@@ -22,30 +22,30 @@ process {
     // Process-specific resource requirements
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
-        cpus   = { check_max( 1                  , 'cpus'    ) }
-        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+        cpus          = { check_max( 1                  , 'cpus'    ) }
+        memory        = { check_max( 6.GB * task.attempt, 'memory'  ) }
+        time          = { check_max( 4.h  * task.attempt, 'time'    ) }
     }
     withLabel:process_low {
-        cpus         = { check_max( 2     * task.attempt, 'cpus'    ) }
-        memory       = { check_max( 12.GB * task.attempt, 'memory'  ) }
-        time         = { check_max( 4.h   * task.attempt, 'time'    ) }
+        cpus          = { check_max( 2     * task.attempt, 'cpus'    ) }
+        memory        = { check_max( 12.GB * task.attempt, 'memory'  ) }
+        time          = { check_max( 4.h   * task.attempt, 'time'    ) }
     }
     withLabel:process_medium {
-        cpus         = { check_max( 6     * task.attempt, 'cpus'    ) }
-        memory       = { check_max( 36.GB * task.attempt, 'memory'  ) }
-        time         = { check_max( 8.h   * task.attempt, 'time'    ) }
+        cpus          = { check_max( 6     * task.attempt, 'cpus'    ) }
+        memory        = { check_max( 36.GB * task.attempt, 'memory'  ) }
+        time          = { check_max( 8.h   * task.attempt, 'time'    ) }
     }
     withLabel:process_high {
-        cpus         = { check_max( 12    * task.attempt, 'cpus'    ) }
-        memory       = { check_max( 72.GB * task.attempt, 'memory'  ) }
-        time         = { check_max( 16.h  * task.attempt, 'time'    ) }
+        cpus          = { check_max( 12    * task.attempt, 'cpus'    ) }
+        memory        = { check_max( 72.GB * task.attempt, 'memory'  ) }
+        time          = { check_max( 16.h  * task.attempt, 'time'    ) }
     }
     withLabel:process_long {
-        time         = { check_max( 20.h  * task.attempt, 'time'    ) }
+        time          = { check_max( 20.h  * task.attempt, 'time'    ) }
     }
     withLabel:process_high_memory {
-        memory       = { check_max( 200.GB * task.attempt, 'memory' ) }
+        memory        = { check_max( 200.GB * task.attempt, 'memory' ) }
     }
     withLabel:error_ignore {
         errorStrategy = 'ignore'
@@ -55,43 +55,43 @@ process {
         maxRetries    = 2
     }
     withName: 'UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX|SAMTOOLS_STATS' {
-        cpus         = { check_max( 1 * task.attempt, 'cpus' ) }
-        memory       = { check_max( 1.GB * task.attempt, 'memory' ) }
+        cpus            = { check_max( 1 * task.attempt, 'cpus' ) }
+        memory          = { check_max( 1.GB * task.attempt, 'memory' ) }
     }
     withName: 'FASTQC'{
-        cpus         = { check_max( 4 * task.attempt, 'cpus' ) }
-        memory       = { check_max( 4.GB * task.attempt, 'memory' ) }
+        cpus            = { check_max( 4 * task.attempt, 'cpus' ) }
+        memory          = { check_max( 4.GB * task.attempt, 'memory' ) }
     }
     withName: 'FASTP'{
-        cpus         = { check_max( 12 * task.attempt, 'cpus' ) }
-        memory       = { check_max( 4.GB * task.attempt, 'memory' ) }
+        cpus            = { check_max( 12 * task.attempt, 'cpus' ) }
+        memory          = { check_max( 4.GB * task.attempt, 'memory' ) }
     }
     withName: 'BWAMEM1_MEM|BWAMEM2_MEM' {
-        cpus         = { check_max( 24 * task.attempt, 'cpus' ) }
-        memory       = { check_max( 30.GB * task.attempt, 'memory' ) }
+        cpus            = { check_max( 24 * task.attempt, 'cpus' ) }
+        memory          = { check_max( 30.GB * task.attempt, 'memory' ) }
     }
     withName: 'GATK4_MARKDUPLICATES|GATK4_MARKDUPLICATESSPARK' {
-        cpus        = { check_max( 6 * task.attempt, 'cpus' ) }
-        memory      = { check_max( 30.GB * task.attempt, 'memory' ) }
+        cpus           = { check_max( 6 * task.attempt, 'cpus' ) }
+        memory         = { check_max( 30.GB * task.attempt, 'memory' ) }
     }
     withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK|GATK4_GATHERBQSRREPORTS'{
-        cpus         = { check_max( 2 * task.attempt, 'cpus' ) }
-        memory       = { check_max( 4.GB * task.attempt, 'memory' ) }
+        cpus            = { check_max( 2 * task.attempt, 'cpus' ) }
+        memory          = { check_max( 4.GB * task.attempt, 'memory' ) }
     }
     withName:'MOSDEPTH'{
-        cpus         = { check_max( 4 * task.attempt, 'cpus' ) }
-        memory       = { check_max( 4.GB * task.attempt, 'memory' ) }
+        cpus            = { check_max( 4 * task.attempt, 'cpus' ) }
+        memory          = { check_max( 4.GB * task.attempt, 'memory' ) }
     }
     withName:'STRELKA.*|MANTA.*' {
         errorStrategy   = { task.exitStatus in [143,137,104,134,139,140,247,1] ? 'retry' : 'finish' }
         cpus            = { check_max( 10 * task.attempt, 'cpus' ) }
         memory          = { check_max( 8.GB * task.attempt, 'memory' ) }
     }
     withName: 'FREEBAYES' {
-        cpus         = { check_max( 1 * task.attempt, 'cpus' ) }
+        cpus            = { check_max( 1 * task.attempt, 'cpus' ) }
     }
     withName:'SAMTOOLS_CONVERT'{
-        memory       = { check_max( 4.GB * task.attempt, 'memory' ) }
+        memory          = { check_max( 4.GB * task.attempt, 'memory' ) }
     }
     withName:'GATK4_MERGEVCFS'{
         cpus            = { check_max( 2 * task.attempt, 'cpus' ) }
@@ -102,5 +102,3 @@ process {
         memory          = { check_max( 12.GB * task.attempt, 'memory' ) }
     }
 }
-
-

conf/test.config

@@ -51,208 +51,6 @@ params {
     schema_ignore_params = 'genomes,test_data,snpeff_version,vep_version'
 }
 
-profiles {
-    annotation {
-        params.input                  = "${projectDir}/tests/csv/3.0/vcf_single.csv"
-        params.step                   = 'annotate'
-        params.tools                  = null // vep, snpeff and/or merge should be specified on the command line
-    }
-    no_intervals {
-        params.intervals              = null
-        params.no_intervals           = true
-        params.tools                  = null
-    }
-    pair {
-        params.input                  = "${projectDir}/tests/csv/3.0/fastq_pair.csv"
-        params.tools                  = null
-    }
-    markduplicates_bam {
-        params.input                  = "${projectDir}/tests/csv/3.0/mapped_single_bam.csv"
-        params.step                   = 'markduplicates'
-        params.tools                  = null
-    }
-    markduplicates_cram {
-        params.input                  = "${projectDir}/tests/csv/3.0/mapped_single_cram.csv"
-        params.step                   = 'markduplicates'
-        params.tools                  = null
-    }
-    prepare_recalibration_bam {
-        params.input                  = "${projectDir}/tests/csv/3.0/mapped_single_bam.csv"
-        params.step                   = 'prepare_recalibration'
-        params.tools                  = null
-    }
-    prepare_recalibration_cram {
-        params.input                  = "${projectDir}/tests/csv/3.0/mapped_single_cram.csv"
-        params.step                   = 'prepare_recalibration'
-        params.tools                  = null
-    }
-    recalibrate_bam {
-        params.input                  = "${projectDir}/tests/csv/3.0/prepare_recalibration_single_bam.csv"
-        params.step                   = 'recalibrate'
-        params.tools                  = null
-    }
-    recalibrate_cram {
-        params.input                  = "${projectDir}/tests/csv/3.0/prepare_recalibration_single_cram.csv"
-        params.step                   = 'recalibrate'
-        params.tools                  = null
-    }
-    save_bam_mapped {
-        params.save_bam_mapped        = true
-        params.tools                  = null
-    }
-    skip_bqsr {
-        params.skip_tools             = "baserecalibrator"
-        params.tools                  = null
-    }
-    skip_markduplicates {
-        params.skip_tools             = "markduplicates"
-        params.tools                  = null
-    }
-    split_fastq {
-        params.save_split_fastqs      = true
-        params.split_fastq            = 150000
-        params.tools                  = null
-    }
-    targeted {
-        params.intervals              = params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed']
-        params.nucleotides_per_second = 20
-        params.tools                  = null
-        params.wes                    = true
-    }
-    tools {
-        params.input                  = "${projectDir}/tests/csv/3.0/recalibrated.csv"
-        params.dbsnp                  = params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz']
-        params.fasta                  = params.test_data['homo_sapiens']['genome']['genome_21_fasta']
-        params.germline_resource      = params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz']
-        params.intervals              = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed']
-        params.pon                    = params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz']
-        params.nucleotides_per_second = 20
-        params.step                   = 'variant_calling'
-        params.tools                  = null
-        params.wes                    = true
-    }
-    tools_germline {
-        params.input                  = "${projectDir}/tests/csv/3.0/recalibrated_germline.csv"
-        params.dbsnp                  = params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz']
-        params.fasta                  = params.test_data['homo_sapiens']['genome']['genome_21_fasta']
-        params.intervals              = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed']
-        params.known_indels           = params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz']
-        params.nucleotides_per_second = 20
-        params.step                   = 'variant_calling'
-        params.tools                  = null
-        params.wes                    = true
-    }
-    tools_tumoronly {
-        params.input                  = "${projectDir}/tests/csv/3.0/recalibrated_tumoronly.csv"
-        params.dbsnp                  = params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz']
-        params.fasta                  = params.test_data['homo_sapiens']['genome']['genome_21_fasta']
-        params.germline_resource      = params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz']
-        params.intervals              = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed']
-        params.pon                    = params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz']
-        params.nucleotides_per_second = 20
-        params.step                   = 'variant_calling'
-        params.tools                  = null
-        params.wes                    = true
-    }
-    tools_somatic {
-        params.input                  = "${projectDir}/tests/csv/3.0/recalibrated_somatic.csv"
-        params.chr_dir                = params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir']
-        params.dbsnp                  = params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz']
-        params.fasta                  = params.test_data['homo_sapiens']['genome']['genome_21_fasta']
-        params.germline_resource      = params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz']
-        params.intervals              = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed']
-        params.pon                    = params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz']
-        params.nucleotides_per_second = 20
-        params.step                   = 'variant_calling'
-        params.tools                  = null
-        params.wes                    = true
-    }
-    // can only be tested locally due to too large cram files for GHA
-    // download corresponding input files (ascat_somatic.csv) from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/
-    // test works only without chromosome annotated loci files available at https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS
-    tools_somatic_ascat{
-        params.input                  = "${baseDir}/tests/csv/3.0/ascat_somatic.csv"
-        params.genome                 = 'GATK.GRCh37'
-        params.igenomes_ignore        = false
-        params.ascat_chromosomes      = 'c("21", "22")'
-        params.ascat_loci             = "/mnt/volume/repos/modules/test_ascat2/G1000_loci_hg19.zip"
-        params.ascat_min_base_qual    = 30
-        params.chr_dir                = params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir']
-        params.germline_resource      = params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz']
-        params.intervals              = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed']
-        params.joint_germline         = true
-        params.step                   = 'variant_calling'
-        params.tools                  = 'ascat'
-        params.wes                    = false
-    }
-    trimming {
-        params.clip_r1                = 1
-        params.clip_r2                = 1
-        params.three_prime_clip_r1    = 1
-        params.three_prime_clip_r2    = 1
-        params.tools                  = null
-        params.trim_fastq             = true
-    }
-    umi {
-        params.input                  = "${projectDir}/tests/csv/3.0/fastq_umi.csv"
-        params.tools                  = null
-        params.umi_read_structure     = '+T 7M1S+T'
-    }
-    use_gatk_spark {
-        params.tools                  = null
-        params.use_gatk_spark         = 'baserecalibrator,markduplicates'
-    }
-    variantcalling_channels {
-        params.input                  = "${projectDir}/tests/csv/3.0/recalibrated.csv"
-        params.fasta                  = params.test_data['homo_sapiens']['genome']['genome_21_fasta']
-        params.intervals              = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed']
-        params.nucleotides_per_second = 20
-        params.step                   = 'variant_calling'
-        params.tools                  = null
-        params.wes                    = true
-    }
-    alignment_to_fastq {
-        params.input                  = "${projectDir}/tests/csv/3.0/bam_for_remapping.csv"
-        params.tools                  = null
-    }
-}
-
-process {
-    withName:'FREEC_SOMATIC'{
-        ext.args = {
-            [
-                "sample":[
-                    inputformat: 'pileup',
-                    mateorientation: 'FR'
-                ],
-                "general" :[
-                    bedgraphoutput: "TRUE",
-                    noisydata: "TRUE",
-                    minexpectedgc: "0",
-                    readcountthreshold: "1",
-                    sex: meta.sex,
-                    window: "10",
-                    ],
-                "control":[
-                    inputformat: "pileup",
-                    mateorientation: "FR"
-                ]
-            ]
-        }
-    }
-
-    if (params.tools && params.tools.split(',').contains('mutect2')) {
-        withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING:MUTECT2'{
-            //sample name from when the test data was generated
-            ext.args = { "--f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz --normal-sample normal " }
-        }
-    }
-
-    withName: 'FILTERVARIANTTRANCHES'{
-        ext.args         = { "--info-key CNN_1D --indel-tranche 0" }
-    }
-}
-
 // Enable container engines/virtualisation envs for CI testing
 // only works when specified with the profile ENV
 // otherwise tests can be done with the regular provided profiles

conf/test_alignment_to_fastq.config

@@ -0,0 +1,15 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/sarek -profile test,<extra_test_profile>,<docker/singularity> --outdir <OUTDIR>
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+params {
+    input = "${projectDir}/tests/csv/3.0/bam_for_remapping.csv"
+    tools = null
+}

conf/test_annotation.config

@@ -0,0 +1,16 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/sarek -profile test,<extra_test_profile>,<docker/singularity> --outdir <OUTDIR>
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+params {
+    input = "${projectDir}/tests/csv/3.0/vcf_single.csv"
+    step  = 'annotate'
+    tools = null // vep, snpeff and/or merge should be specified on the command line
+}

conf/test_markduplicates_bam.config

@@ -0,0 +1,16 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/sarek -profile test,<extra_test_profile>,<docker/singularity> --outdir <OUTDIR>
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+params {
+    input = "${projectDir}/tests/csv/3.0/mapped_single_bam.csv"
+    step  = 'markduplicates'
+    tools = null
+}

conf/test_markduplicates_cram.config

@@ -0,0 +1,16 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/sarek -profile test,<extra_test_profile>,<docker/singularity> --outdir <OUTDIR>
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+params {
+    input = "${projectDir}/tests/csv/3.0/mapped_single_cram.csv"
+    step  = 'markduplicates'
+    tools = null
+}