diff --git a/modules.json b/modules.json index cd1663906c..6dffdac102 100644 --- a/modules.json +++ b/modules.json @@ -19,16 +19,16 @@ "git_sha": "c8877835c288eb32b2ad1810d38a78e83e791f3d" }, "multiqc": { - "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d" + "git_sha": "c5235a983d454787fa0c3247b02086969217163b" }, "samtools/faidx": { - "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d" + "git_sha": "c5235a983d454787fa0c3247b02086969217163b" }, "samtools/merge": { - "git_sha": "adfb8a3d6541f363aec83df16df873cbb767b388" + "git_sha": "c5235a983d454787fa0c3247b02086969217163b" }, "seqkit/split2": { - "git_sha": "65ab646870c4ff74322b4fff22ad51b190791a2c" + "git_sha": "c5235a983d454787fa0c3247b02086969217163b" }, "snpeff": { "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d" @@ -40,8 +40,8 @@ "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d" }, "trimgalore": { - "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d" + "git_sha": "c5235a983d454787fa0c3247b02086969217163b" } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/modules/multiqc/main.nf b/modules/nf-core/modules/multiqc/main.nf index da78080024..8b6d6f0c5e 100644 --- a/modules/nf-core/modules/multiqc/main.nf +++ b/modules/nf-core/modules/multiqc/main.nf @@ -10,11 +10,11 @@ process MULTIQC { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) } - conda (params.enable_conda ? "bioconda::multiqc=1.10.1" : null) + conda (params.enable_conda ? 'bioconda::multiqc=1.11' : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/multiqc:1.10.1--py_0" + container "https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0" } else { - container "quay.io/biocontainers/multiqc:1.10.1--py_0" + container "quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0" } input: diff --git a/modules/nf-core/modules/samtools/faidx/main.nf b/modules/nf-core/modules/samtools/faidx/main.nf index 6c023f1cd8..a89ff2bbb6 100644 --- a/modules/nf-core/modules/samtools/faidx/main.nf +++ b/modules/nf-core/modules/samtools/faidx/main.nf @@ -11,11 +11,11 @@ process SAMTOOLS_FAIDX { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) } - conda (params.enable_conda ? "bioconda::samtools=1.12" : null) + conda (params.enable_conda ? 'bioconda::samtools=1.13' : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0" + container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0" } else { - container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0" + container "quay.io/biocontainers/samtools:1.13--h8c37831_0" } input: diff --git a/modules/nf-core/modules/samtools/merge/main.nf b/modules/nf-core/modules/samtools/merge/main.nf index 23b31e2f9a..0182b9fd52 100644 --- a/modules/nf-core/modules/samtools/merge/main.nf +++ b/modules/nf-core/modules/samtools/merge/main.nf @@ -11,11 +11,11 @@ process SAMTOOLS_MERGE { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::samtools=1.12" : null) + conda (params.enable_conda ? 'bioconda::samtools=1.13' : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0" + container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0" } else { - container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0" + container "quay.io/biocontainers/samtools:1.13--h8c37831_0" } input: diff --git a/modules/nf-core/modules/seqkit/split2/main.nf b/modules/nf-core/modules/seqkit/split2/main.nf index 4c516c9344..5eeb0ad08d 100644 --- a/modules/nf-core/modules/seqkit/split2/main.nf +++ b/modules/nf-core/modules/seqkit/split2/main.nf @@ -12,12 +12,12 @@ process SEQKIT_SPLIT2 { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::seqkit=0.16.0" : null) + conda (params.enable_conda ? 'bioconda::seqkit=0.16.1' : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/seqkit:0.16.0--h9ee0642_0" + container "https://depot.galaxyproject.org/singularity/seqkit:0.16.1--h9ee0642_0" } else { - container "quay.io/biocontainers/seqkit:0.16.0--h9ee0642_0" + container "quay.io/biocontainers/seqkit:0.16.1--h9ee0642_0" } input: diff --git a/modules/nf-core/modules/trimgalore/main.nf b/modules/nf-core/modules/trimgalore/main.nf index 44b36e7148..3c16d66fee 100644 --- a/modules/nf-core/modules/trimgalore/main.nf +++ b/modules/nf-core/modules/trimgalore/main.nf @@ -11,11 +11,11 @@ process TRIMGALORE { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } - conda (params.enable_conda ? "bioconda::trim-galore=0.6.6" : null) + conda (params.enable_conda ? 'bioconda::trim-galore=0.6.7' : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.6--0" + container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0" } else { - container "quay.io/biocontainers/trim-galore:0.6.6--0" + container "quay.io/biocontainers/trim-galore:0.6.7--hdfd78af_0" } input: diff --git a/subworkflows/local/build_indices.nf b/subworkflows/local/build_indices.nf index 2063e6a01f..201b2ce6a1 100644 --- a/subworkflows/local/build_indices.nf +++ b/subworkflows/local/build_indices.nf @@ -19,18 +19,18 @@ params.tabix_pon_options = [:] // Initialize channels based on params or indices that were just built -include { BUILD_INTERVALS } from '../../modules/local/build_intervals/main' addParams(options: params.build_intervals_options) -include { BWA_INDEX as BWAMEM1_INDEX } from '../../modules/nf-core/modules/bwa/index/main' addParams(options: params.bwa_index_options) -include { BWAMEM2_INDEX } from '../../modules/nf-core/modules/bwamem2/index/main' addParams(options: params.bwamem2_index_options) -include { CREATE_INTERVALS_BED } from '../../modules/local/create_intervals_bed/main' addParams(options: params.create_intervals_bed_options) -include { GATK4_CREATESEQUENCEDICTIONARY as GATK4_DICT } from '../../modules/nf-core/modules/gatk4/createsequencedictionary/main' addParams(options: params.gatk4_dict_options) -include { MSISENSORPRO_SCAN } from '../../modules/local/msisensorpro/scan/main' addParams(options: params.msisensorpro_scan_options) -include { SAMTOOLS_FAIDX } from '../../modules/nf-core/modules/samtools/faidx/main' addParams(options: params.samtools_faidx_options) -include { TABIX_BGZIPTABIX } from '../../modules/nf-core/modules/tabix/bgziptabix/main' addParams(options: params.bgziptabix_options) -include { TABIX_TABIX as TABIX_DBSNP } from '../../modules/nf-core/modules/tabix/tabix/main' addParams(options: params.tabix_dbsnp_options) -include { TABIX_TABIX as TABIX_GERMLINE_RESOURCE } from '../../modules/nf-core/modules/tabix/tabix/main' addParams(options: params.tabix_germline_resource_options) -include { TABIX_TABIX as TABIX_KNOWN_INDELS } from '../../modules/nf-core/modules/tabix/tabix/main' addParams(options: params.tabix_known_indels_options) -include { TABIX_TABIX as TABIX_PON } from '../../modules/nf-core/modules/tabix/tabix/main' addParams(options: params.tabix_pon_options) +include { BUILD_INTERVALS } from '../../modules/local/build_intervals/main' addParams(options: params.build_intervals_options) +include { BWA_INDEX as BWAMEM1_INDEX } from '../../modules/nf-core/modules/bwa/index/main' addParams(options: params.bwa_index_options) +include { BWAMEM2_INDEX } from '../../modules/nf-core/modules/bwamem2/index/main' addParams(options: params.bwamem2_index_options) +include { CREATE_INTERVALS_BED } from '../../modules/local/create_intervals_bed/main' addParams(options: params.create_intervals_bed_options) +include { GATK4_CREATESEQUENCEDICTIONARY } from '../../modules/nf-core/modules/gatk4/createsequencedictionary/main' addParams(options: params.gatk4_dict_options) +include { MSISENSORPRO_SCAN } from '../../modules/local/msisensorpro/scan/main' addParams(options: params.msisensorpro_scan_options) +include { SAMTOOLS_FAIDX } from '../../modules/nf-core/modules/samtools/faidx/main' addParams(options: params.samtools_faidx_options) +include { TABIX_BGZIPTABIX } from '../../modules/nf-core/modules/tabix/bgziptabix/main' addParams(options: params.bgziptabix_options) +include { TABIX_TABIX as TABIX_DBSNP } from '../../modules/nf-core/modules/tabix/tabix/main' addParams(options: params.tabix_dbsnp_options) +include { TABIX_TABIX as TABIX_GERMLINE_RESOURCE } from '../../modules/nf-core/modules/tabix/tabix/main' addParams(options: params.tabix_germline_resource_options) +include { TABIX_TABIX as TABIX_KNOWN_INDELS } from '../../modules/nf-core/modules/tabix/tabix/main' addParams(options: params.tabix_known_indels_options) +include { TABIX_TABIX as TABIX_PON } from '../../modules/nf-core/modules/tabix/tabix/main' addParams(options: params.tabix_pon_options) workflow BUILD_INDICES { take: @@ -52,64 +52,64 @@ workflow BUILD_INDICES { if (params.aligner == "bwa-mem") (result_bwa, version_bwa) = BWAMEM1_INDEX(fasta) else (result_bwa, version_bwa) = BWAMEM2_INDEX(fasta) - result_dict = Channel.empty() + result_dict = Channel.empty() version_dict = Channel.empty() if (!(params.dict) && !('annotate' in step) && !('controlfreec' in step)) - (result_dict, version_dict) = GATK4_DICT(fasta) + (result_dict, version_dict) = GATK4_CREATESEQUENCEDICTIONARY(fasta) - result_fai = Channel.empty() - if (fasta_fai) result_fai = fasta_fai + result_fai = Channel.empty() version_fai = Channel.empty() + if (fasta_fai) result_fai = fasta_fai if (!(params.fasta_fai) && !('annotate' in step)) (result_fai, version_fai) = SAMTOOLS_FAIDX(fasta) - result_dbsnp_tbi = Channel.empty() + result_dbsnp_tbi = Channel.empty() version_dbsnp_tbi = Channel.empty() if (!(params.dbsnp_tbi) && params.dbsnp && ('mapping' in step || 'preparerecalibration' in step || 'controlfreec' in tools || 'haplotypecaller' in tools|| 'mutect2' in tools || 'tnscope' in tools)) { - dbsnp_id = dbsnp.map {it -> [[id:"$it.baseName"], it]} + dbsnp_id = dbsnp.map{ it -> [[id:it[0].baseName], it] } (result_dbsnp_tbi, version_dbsnp_tbi) = TABIX_DBSNP(dbsnp_id) - result_dbsnp_tbi = result_dbsnp_tbi.map {meta, tbi -> [tbi]} + result_dbsnp_tbi = result_dbsnp_tbi.map{ meta, tbi -> [tbi] } } - result_target_bed = Channel.empty() + result_target_bed = Channel.empty() version_target_bed = Channel.empty() if ((params.target_bed) && ('manta' in tools || 'strelka' in tools)) { - target_bed_id = target_bed.map {it -> [[id:"$it.baseName"], it]} + target_bed_id = target_bed.map{ it -> [[id:it[0].baseName], it] } (result_target_bed, version_target_bed) = TABIX_BGZIPTABIX(target_bed_id) - result_target_bed = result_target_bed.map {meta, bed, tbi -> [bed, tbi]} + result_target_bed = result_target_bed.map{ meta, bed, tbi -> [bed, tbi] } } - result_germline_resource_tbi = Channel.empty() + result_germline_resource_tbi = Channel.empty() version_germline_resource_tbi = Channel.empty() if (!(params.germline_resource_tbi) && params.germline_resource && 'mutect2' in tools) { - germline_resource_id = germline_resource.map {it -> [[id:"$it.baseName"], it]} + germline_resource_id = germline_resource.map{ it -> [[id:it[0].baseName], it] } (result_germline_resource_tbi, version_germline_resource_tbi) = TABIX_GERMLINE_RESOURCE(germline_resource_id) } - result_known_indels_tbi = Channel.empty() + result_known_indels_tbi = Channel.empty() version_known_indels_tbi = Channel.empty() if (!(params.known_indels_tbi) && params.known_indels && ('mapping' in step || 'preparerecalibration' in step)) { - known_indels_id = known_indels.map {it -> [[id:"$it.baseName"], it]} + known_indels_id = known_indels.map{ it -> [[id:it[0].baseName], it] } (result_known_indels_tbi, version_known_indels_tbi) = TABIX_KNOWN_INDELS(known_indels_id) - result_known_indels_tbi = result_known_indels_tbi.map {meta, tbi -> [tbi]} + result_known_indels_tbi = result_known_indels_tbi.map{ meta, tbi -> [tbi] } } - result_msisensorpro_scan = Channel.empty() + result_msisensorpro_scan = Channel.empty() version_msisensorpro_scan = Channel.empty() if ('msisensorpro' in tools) (result_msisensorpro_scan, version_msisensorpro_scan) = MSISENSORPRO_SCAN(fasta) - result_pon_tbi = Channel.empty() + result_pon_tbi = Channel.empty() version_pon_tbi = Channel.empty() if (!(params.pon_tbi) && params.pon && ('tnscope' in tools || 'mutect2' in tools)) { - pon_id = pon.map {it -> [[id:"$it.baseName"], it]} + pon_id = pon.map{ it -> [[id:it[0].baseName], it] } (result_pon_tbi, version_pon_tbi) = TABIX_PON(pon_id) } result_intervals = Channel.empty() if (params.no_intervals) { file("${params.outdir}/no_intervals.bed").text = "no_intervals\n" - result_intervals = Channel.from(file("${params.outdir}/no_intervals.bed")) + result_intervals = Channel.fromPath(file("${params.outdir}/no_intervals.bed")) } else if (!('annotate' in step) && !('controlfreec' in step)) if (!params.intervals) result_intervals = CREATE_INTERVALS_BED(BUILD_INTERVALS(result_fai)) @@ -118,7 +118,7 @@ workflow BUILD_INDICES { if (!params.no_intervals) { result_intervals = result_intervals.flatten() - .map { intervalFile -> + .map{ intervalFile -> def duration = 0.0 for (line in intervalFile.readLines()) { final fields = line.split('\t')