From a7b396e623b611cc0a0f8243733d067a8495b51d Mon Sep 17 00:00:00 2001 From: Sander Boymans Date: Thu, 21 May 2020 12:13:16 +0200 Subject: [PATCH 01/22] First draft --- Manta/1.6.0/Manta.nf | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 Manta/1.6.0/Manta.nf diff --git a/Manta/1.6.0/Manta.nf b/Manta/1.6.0/Manta.nf new file mode 100644 index 00000000..2d1b82c2 --- /dev/null +++ b/Manta/1.6.0/Manta.nf @@ -0,0 +1,26 @@ +process Manta { + tag {"Manta ConfigAndRun ${sample_id}"} + label 'Manta_1_6_0' + label 'Manta_1_6_0_ConfigAndRun' + //container = 'container_url' + shell = ['/bin/bash', '-euo', 'pipefail'] + + input: + tuple (sample_id, path(bam_file), path(bai_file)) + + output: + tuple (sample_id, path("*.candidateSmallIndels.*"),path("*.candidateSV.*"),path("*.diploidSV.*"), emit: manta_vcfs ) + + script: + """ + ${params.manta_path}/configManta.py --referenceFasta ${params.genome_fasta} --runDir . --bam $bam_file + ${params.manta_path}/runWorkflow.py -m local -j ${task.cpus} + + mv Manta/results/variants/candidateSmallIndels.vcf.gz Manta_${sample_id}.candidateSmallIndels.vcf.gz + mv Manta/results/variants/candidateSmallIndels.vcf.gz.tbi Manta_${sample_id}.candidateSmallIndels.vcf.gz.tbi + mv Manta/results/variants/candidateSV.vcf.gz Manta_${sample_id}.candidateSV.vcf.gz + mv Manta/results/variants/candidateSV.vcf.gz.tbi Manta_${sample_id}.candidateSV.vcf.gz.tbi + mv Manta/results/variants/diploidSV.vcf.gz Manta_${sample_id}.diploidSV.vcf.gz + mv Manta/results/variants/diploidSVSV.vcf.gz.tbi Manta_${sample_id}.diploidSV.vcf.gz.tbi + """ +} From e962793fdcadc9561bc3035bf6cebc5e67b35cd7 Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Wed, 27 May 2020 16:31:35 +0200 Subject: [PATCH 02/22] Add BaseRecalibrator, including PrintReads. --- GATK/3.8-1-0-gf15c1c3ef/BaseRecalibrator.nf | 32 +++++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 GATK/3.8-1-0-gf15c1c3ef/BaseRecalibrator.nf diff --git a/GATK/3.8-1-0-gf15c1c3ef/BaseRecalibrator.nf b/GATK/3.8-1-0-gf15c1c3ef/BaseRecalibrator.nf new file mode 100644 index 00000000..419c0539 --- /dev/null +++ b/GATK/3.8-1-0-gf15c1c3ef/BaseRecalibrator.nf @@ -0,0 +1,32 @@ +process BaseRecalibrator { + tag {"GATK BaseRecalibrator ${sample_id} - ${chr}"} + label 'GATK_3_8_1_0_gf15c1c3ef' + label 'GATK_3_8_1_0_gf15c1c3ef_BaseRecalibrator' + container = 'quay.io/biocontainers/gatk:3.8--py27_1' + shell = ['/bin/bash', '-euo', 'pipefail'] + + input: + tuple(sample_id, path(bam_file), path(bai_file), chr) + + output: + tuple(sample_id, path("${bam_file.baseName}.bqsr.${chr}.bam"), path("${bam_file.baseName}.bqsr.${chr}.bai"), emit: bam_file) + + script: + """ + java -Xmx${task.memory.toGiga()-4}G -jar $params.gatk_path -T BaseRecalibrator \ + --num_cpu_threads_per_data_thread ${task.cpus} \ + --reference_sequence ${params.genome} \ + --input_file ${bam_file} \ + --intervals ${chr} \ + --out ${bam_file.baseName}.bqsr.${chr}.table \ + ${params.optional} + + java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T PrintReads \ + --num_cpu_threads_per_data_thread ${task.cpus} \ + --reference_sequence ${params.genome} \ + --input_file ${bam_file} \ + --BQSR ${bam_file.baseName}.bqsr.${chr}.table \ + --intervals ${chr} \ + --out ${bam_file.baseName}.bqsr.${chr}.bam + """ +} From a7d04fb578ef9a646cc111f947c534bef7740ffa Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Thu, 4 Jun 2020 11:01:47 +0200 Subject: [PATCH 03/22] Add optional. --- Picard/2.22.0/IntervalListTools.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Picard/2.22.0/IntervalListTools.nf b/Picard/2.22.0/IntervalListTools.nf index d81bde50..838e5801 100644 --- a/Picard/2.22.0/IntervalListTools.nf +++ b/Picard/2.22.0/IntervalListTools.nf @@ -18,7 +18,8 @@ process IntervalListTools { SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW \ SCATTER_COUNT=${params.scatter_count} \ UNIQUE=true \ - + ${params.optional} + for folder in temp*; do mv \$folder/scattered.interval_list \$folder/\$folder\\.interval_list; done """ } From 8db71b5c89b9a9dbd98bb9464fc03f69e3da63ef Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Thu, 4 Jun 2020 13:52:56 +0200 Subject: [PATCH 04/22] Add HaplotypeCallerGVCF --- GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf | 26 ++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf b/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf index 3c42714f..03d5f594 100644 --- a/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf +++ b/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf @@ -22,3 +22,29 @@ process HaplotypeCaller { ${params.optional} """ } + +process HaplotypeCallerGVCF { + tag {"GATK HaplotypeCallerGVCF ${sample_id} - ${interval_file.baseName}"} + label 'GATK_3_8_1_0_gf15c1c3ef' + label 'GATK_3_8_1_0_gf15c1c3ef_HaplotypeCaller' + container = 'quay.io/biocontainers/gatk:3.8--py27_1' + shell = ['/bin/bash', '-euo', 'pipefail'] + + input: + tuple(sample_id, path(bam_file), path(bai_file), path(interval_file)) + + output: + tuple(val(sample_id), file("${sample_id}.${interval_file.baseName}.g.vcf."), file("${sample_id}.${interval_file.baseName}.g.vcf.idx"), emit: vcf_file) + + script: + """ + java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T HaplotypeCaller \ + --reference_sequence ${params.genome} \ + --input_file ${bam_file} \ + --intervals ${interval_file} \ + --out ${analysis_id}.${interval_file.baseName}.g.vcf \ + --emitRefConfidence GVCF \ + --GVCFGQBands 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,70,80,90,99 \ + ${params.optional} + """ +} \ No newline at end of file From ad2b8176acdd439ee9936b3ed3e22ce3af203c83 Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Thu, 4 Jun 2020 14:30:45 +0200 Subject: [PATCH 05/22] Add gvcf tools. --- GATK/3.8-1-0-gf15c1c3ef/CombineVariants.nf | 20 ++++++++++++++++++++ GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf | 2 +- 2 files changed, 21 insertions(+), 1 deletion(-) diff --git a/GATK/3.8-1-0-gf15c1c3ef/CombineVariants.nf b/GATK/3.8-1-0-gf15c1c3ef/CombineVariants.nf index a2f7a4f0..5ed12ece 100644 --- a/GATK/3.8-1-0-gf15c1c3ef/CombineVariants.nf +++ b/GATK/3.8-1-0-gf15c1c3ef/CombineVariants.nf @@ -17,3 +17,23 @@ process CombineVariants { java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T CombineVariants --reference_sequence ${params.genome} -V ${input_files} --out ${analysis_id}.vcf ${params.optional} """ } + +process CombineVariantsGVCF { + tag {"GATK CombineVariantsGVCF ${sample_id}"} + label 'GATK_3_8_1_0_gf15c1c3ef' + label 'GATK_3_8_1_0_gf15c1c3ef_CombineVariantsGVCF' + container = 'quay.io/biocontainers/gatk:3.8--py27_1' + shell = ['/bin/bash', '-euo', 'pipefail'] + + input: + tuple(sample_id, path(vcf_files), path(vcf_idx_files)) + + output: + tuple(sample_id, path("${sample_id}.g.vcf"), path("${sample_id}.g.vcf.idx"), emit:vcf_file) + + script: + def input_files = vcf_files.collect{"$it"}.join(" -V ") + """ + java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T CombineVariants --reference_sequence ${params.genome} -V ${input_files} --out ${sample_id}.g.vcf ${params.optional} + """ +} diff --git a/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf b/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf index 03d5f594..dafb3e67 100644 --- a/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf +++ b/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf @@ -26,7 +26,7 @@ process HaplotypeCaller { process HaplotypeCallerGVCF { tag {"GATK HaplotypeCallerGVCF ${sample_id} - ${interval_file.baseName}"} label 'GATK_3_8_1_0_gf15c1c3ef' - label 'GATK_3_8_1_0_gf15c1c3ef_HaplotypeCaller' + label 'GATK_3_8_1_0_gf15c1c3ef_HaplotypeCallerGVCF' container = 'quay.io/biocontainers/gatk:3.8--py27_1' shell = ['/bin/bash', '-euo', 'pipefail'] From 0513c77cf0614f8a8420b12e57b1d3c312c6b379 Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Fri, 5 Jun 2020 12:35:41 +0200 Subject: [PATCH 06/22] Add CatVariants and GenotypeGVCFs --- GATK/3.8-1-0-gf15c1c3ef/CatVariants.nf | 19 +++++++++++++++++++ GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf | 19 +++++++++++++++++++ 2 files changed, 38 insertions(+) create mode 100644 GATK/3.8-1-0-gf15c1c3ef/CatVariants.nf create mode 100644 GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf diff --git a/GATK/3.8-1-0-gf15c1c3ef/CatVariants.nf b/GATK/3.8-1-0-gf15c1c3ef/CatVariants.nf new file mode 100644 index 00000000..98ffe9a6 --- /dev/null +++ b/GATK/3.8-1-0-gf15c1c3ef/CatVariants.nf @@ -0,0 +1,19 @@ +process CatVariantsGVCF { + tag {"GATK CatVariantsGVCF ${sample_id}"} + label 'GATK_3_8_1_0_gf15c1c3ef' + label 'GATK_3_8_1_0_gf15c1c3ef_CatVariantsGVCF' + container = 'quay.io/biocontainers/gatk:3.8--py27_1' + shell = ['/bin/bash', '-euo', 'pipefail'] + + input: + tuple(sample_id, path(gvcf_files), path(gvcf_idx_files)) + + output: + tuple(sample_id, path("${sample_id}.g.vcf"), path("${sample_id}.g.vcf.idx"), emit:vcf_file) + + script: + def input_files = gvcf_files.collect{"$it"}.join(" -V ") + """ + java -Xmx${task.memory.toGiga()-4}G -cp ${params.gatk_path} org.broadinstitute.gatk.tools.CatVariants --reference ${params.genome} -V ${input_files} --out ${sample_id}.g.vcf ${params.optional} + """ +} \ No newline at end of file diff --git a/GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf b/GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf new file mode 100644 index 00000000..84c95e53 --- /dev/null +++ b/GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf @@ -0,0 +1,19 @@ +process GenotypeGVCFs { + tag {"GATK GenotypeGVCFs ${analysis_id}"} + label 'GATK_3_8_1_0_gf15c1c3ef' + label 'GATK_3_8_1_0_gf15c1c3ef_GenotypeGVCFs' + container = 'quay.io/biocontainers/gatk:3.8--py27_1' + shell = ['/bin/bash', '-euo', 'pipefail'] + + input: + tuple(analysis_id, path(gvcf_files), path(gvcf_idx_files)) + + output: + tuple(analysis_id, path("${analysis_id}.vcf"), path("${analysis_id}.vcf.idx"), emit:vcf_file) + + script: + def input_files = gvcf_files.collect{"$it"}.join(" -V ") + """ + java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T GenotypeGVCFs --reference_sequence ${params.genome} -V ${input_files} --out ${analysis_id}.vcf ${params.optional} + """ +} \ No newline at end of file From 27cc98d285111ab0edf35f2f1f51cc4f2e8ac56a Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Fri, 5 Jun 2020 12:39:55 +0200 Subject: [PATCH 07/22] Remove GVCFGQBands --- GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf b/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf index dafb3e67..7330014c 100644 --- a/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf +++ b/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf @@ -44,7 +44,6 @@ process HaplotypeCallerGVCF { --intervals ${interval_file} \ --out ${analysis_id}.${interval_file.baseName}.g.vcf \ --emitRefConfidence GVCF \ - --GVCFGQBands 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,70,80,90,99 \ ${params.optional} """ } \ No newline at end of file From ceb588a82c785339fb7b311d754045cab871eb7d Mon Sep 17 00:00:00 2001 From: rernst Date: Tue, 9 Jun 2020 11:36:02 +0200 Subject: [PATCH 08/22] Fix modules --- GATK/3.8-1-0-gf15c1c3ef/CatVariants.nf | 4 ++-- GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf | 2 +- GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf | 6 +++--- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/GATK/3.8-1-0-gf15c1c3ef/CatVariants.nf b/GATK/3.8-1-0-gf15c1c3ef/CatVariants.nf index 98ffe9a6..fe5aa5e5 100644 --- a/GATK/3.8-1-0-gf15c1c3ef/CatVariants.nf +++ b/GATK/3.8-1-0-gf15c1c3ef/CatVariants.nf @@ -14,6 +14,6 @@ process CatVariantsGVCF { script: def input_files = gvcf_files.collect{"$it"}.join(" -V ") """ - java -Xmx${task.memory.toGiga()-4}G -cp ${params.gatk_path} org.broadinstitute.gatk.tools.CatVariants --reference ${params.genome} -V ${input_files} --out ${sample_id}.g.vcf ${params.optional} + java -Xmx${task.memory.toGiga()-4}G -cp ${params.gatk_path} org.broadinstitute.gatk.tools.CatVariants --reference ${params.genome} -V ${input_files} --outputFile ${sample_id}.g.vcf ${params.optional} """ -} \ No newline at end of file +} diff --git a/GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf b/GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf index 84c95e53..f352e728 100644 --- a/GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf +++ b/GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf @@ -16,4 +16,4 @@ process GenotypeGVCFs { """ java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T GenotypeGVCFs --reference_sequence ${params.genome} -V ${input_files} --out ${analysis_id}.vcf ${params.optional} """ -} \ No newline at end of file +} diff --git a/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf b/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf index 7330014c..157b8867 100644 --- a/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf +++ b/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf @@ -34,7 +34,7 @@ process HaplotypeCallerGVCF { tuple(sample_id, path(bam_file), path(bai_file), path(interval_file)) output: - tuple(val(sample_id), file("${sample_id}.${interval_file.baseName}.g.vcf."), file("${sample_id}.${interval_file.baseName}.g.vcf.idx"), emit: vcf_file) + tuple(val(sample_id), file("${sample_id}_${interval_file.baseName}.g.vcf"), file("${sample_id}_${interval_file.baseName}.g.vcf.idx"), emit: vcf_file) script: """ @@ -42,8 +42,8 @@ process HaplotypeCallerGVCF { --reference_sequence ${params.genome} \ --input_file ${bam_file} \ --intervals ${interval_file} \ - --out ${analysis_id}.${interval_file.baseName}.g.vcf \ + --out ${sample_id}_${interval_file.baseName}.g.vcf \ --emitRefConfidence GVCF \ ${params.optional} """ -} \ No newline at end of file +} From c494bd9f2181972ca0adc4b2b9f1e627a27faf1a Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Wed, 10 Jun 2020 10:51:45 +0200 Subject: [PATCH 09/22] Update gvcf --- GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf | 9 +++++++-- GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf | 4 ++-- 2 files changed, 9 insertions(+), 4 deletions(-) diff --git a/GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf b/GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf index f352e728..43260b35 100644 --- a/GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf +++ b/GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf @@ -6,7 +6,7 @@ process GenotypeGVCFs { shell = ['/bin/bash', '-euo', 'pipefail'] input: - tuple(analysis_id, path(gvcf_files), path(gvcf_idx_files)) + tuple(analysis_id, path(gvcf_files), path(gvcf_idx_files), path(interval_file)) output: tuple(analysis_id, path("${analysis_id}.vcf"), path("${analysis_id}.vcf.idx"), emit:vcf_file) @@ -14,6 +14,11 @@ process GenotypeGVCFs { script: def input_files = gvcf_files.collect{"$it"}.join(" -V ") """ - java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T GenotypeGVCFs --reference_sequence ${params.genome} -V ${input_files} --out ${analysis_id}.vcf ${params.optional} + java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T GenotypeGVCFs \ + --reference_sequence ${params.genome} \ + -V ${input_files} \ + --out ${analysis_id}.vcf \ + --intervals ${interval_file} \ + ${params.optional} \ """ } diff --git a/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf b/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf index 157b8867..c3f0bf28 100644 --- a/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf +++ b/GATK/3.8-1-0-gf15c1c3ef/HaplotypeCaller.nf @@ -9,7 +9,7 @@ process HaplotypeCaller { tuple(analysis_id, path(bam_files), path(bai_files), path(interval_file)) output: - tuple(val(analysis_id), file("${analysis_id}.${interval_file.baseName}.vcf"), file("${analysis_id}.${interval_file.baseName}.vcf.idx"), emit: vcf_file) + tuple(val(analysis_id), path("${analysis_id}.${interval_file.baseName}.vcf"), path("${analysis_id}.${interval_file.baseName}.vcf.idx"), emit: vcf_file) script: def input_files = bam_files.collect{"$it"}.join(" --input_file ") @@ -34,7 +34,7 @@ process HaplotypeCallerGVCF { tuple(sample_id, path(bam_file), path(bai_file), path(interval_file)) output: - tuple(val(sample_id), file("${sample_id}_${interval_file.baseName}.g.vcf"), file("${sample_id}_${interval_file.baseName}.g.vcf.idx"), emit: vcf_file) + tuple(val(sample_id), path("${sample_id}_${interval_file.baseName}.g.vcf"), path("${sample_id}_${interval_file.baseName}.g.vcf.idx"), path(interval_file), emit: vcf_file) script: """ From cda8347e5eca53d35a79dbc248a9687eac645a41 Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Wed, 10 Jun 2020 12:09:52 +0200 Subject: [PATCH 10/22] Unique names --- GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf b/GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf index 43260b35..1714b61f 100644 --- a/GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf +++ b/GATK/3.8-1-0-gf15c1c3ef/GenotypeGVCFs.nf @@ -9,7 +9,7 @@ process GenotypeGVCFs { tuple(analysis_id, path(gvcf_files), path(gvcf_idx_files), path(interval_file)) output: - tuple(analysis_id, path("${analysis_id}.vcf"), path("${analysis_id}.vcf.idx"), emit:vcf_file) + tuple(analysis_id, path("${analysis_id}_${interval_file.baseName}.vcf"), path("${analysis_id}_${interval_file.baseName}.vcf.idx"), emit:vcf_file) script: def input_files = gvcf_files.collect{"$it"}.join(" -V ") @@ -17,7 +17,7 @@ process GenotypeGVCFs { java -Xmx${task.memory.toGiga()-4}G -jar ${params.gatk_path} -T GenotypeGVCFs \ --reference_sequence ${params.genome} \ -V ${input_files} \ - --out ${analysis_id}.vcf \ + --out ${analysis_id}_${interval_file.baseName}.vcf \ --intervals ${interval_file} \ ${params.optional} \ """ From faa31951be71c3c74f620def99550b201aa07d98 Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Wed, 10 Jun 2020 16:48:13 +0200 Subject: [PATCH 11/22] Add FREEC --- Control-FREEC/11.6/Control-FREEC.nf | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 Control-FREEC/11.6/Control-FREEC.nf diff --git a/Control-FREEC/11.6/Control-FREEC.nf b/Control-FREEC/11.6/Control-FREEC.nf new file mode 100644 index 00000000..80b1a777 --- /dev/null +++ b/Control-FREEC/11.6/Control-FREEC.nf @@ -0,0 +1,17 @@ +process Freec { + tag {"Control-FREEC ${sample_id}"} + label 'Control-FREEC_11_6' + container = 'quay.io/biocontainers/control-freec:11.6--he1b5a44_0' + shell = ['/bin/bash', '-euo', 'pipefail'] + + input: + tuple(sample_id, path(bam_file), path(bai_file)) + + output: + tuple(sample_id, path("*")) + + script: + """ + freec -conf ${params.config} -sample ${bam_file} + """ +} From 05ed063c0bb3cfa3a27c019264ab63c0117b5dcf Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Wed, 10 Jun 2020 16:52:53 +0200 Subject: [PATCH 12/22] Update Freec --- .../Control-FREEC.nf => ControlFREEC/11.6/ControlFREEC.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename Control-FREEC/11.6/Control-FREEC.nf => ControlFREEC/11.6/ControlFREEC.nf (83%) diff --git a/Control-FREEC/11.6/Control-FREEC.nf b/ControlFREEC/11.6/ControlFREEC.nf similarity index 83% rename from Control-FREEC/11.6/Control-FREEC.nf rename to ControlFREEC/11.6/ControlFREEC.nf index 80b1a777..d8e537ec 100644 --- a/Control-FREEC/11.6/Control-FREEC.nf +++ b/ControlFREEC/11.6/ControlFREEC.nf @@ -1,6 +1,6 @@ process Freec { - tag {"Control-FREEC ${sample_id}"} - label 'Control-FREEC_11_6' + tag {"Control_FREEC ${sample_id}"} + label 'Control_FREEC_11_6' container = 'quay.io/biocontainers/control-freec:11.6--he1b5a44_0' shell = ['/bin/bash', '-euo', 'pipefail'] From 674448207a85065cbac17e639991013cd64f6f75 Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Thu, 11 Jun 2020 15:13:11 +0200 Subject: [PATCH 13/22] Update freec --- ControlFREEC/11.5/AssessSignificance.nf | 18 ++++++++++++++++++ ControlFREEC/11.5/Freec.nf | 19 +++++++++++++++++++ ControlFREEC/11.5/MakeGraph.nf | 18 ++++++++++++++++++ ControlFREEC/11.6/ControlFREEC.nf | 17 ----------------- 4 files changed, 55 insertions(+), 17 deletions(-) create mode 100644 ControlFREEC/11.5/AssessSignificance.nf create mode 100644 ControlFREEC/11.5/Freec.nf create mode 100644 ControlFREEC/11.5/MakeGraph.nf delete mode 100644 ControlFREEC/11.6/ControlFREEC.nf diff --git a/ControlFREEC/11.5/AssessSignificance.nf b/ControlFREEC/11.5/AssessSignificance.nf new file mode 100644 index 00000000..da0f9392 --- /dev/null +++ b/ControlFREEC/11.5/AssessSignificance.nf @@ -0,0 +1,18 @@ +process AssessSignificance { + tag {"Control Freec AssessSignificance ${sample_id}"} + label 'ControlFreec_11_5' + label 'ControlFreec_11_5_AssessSignificance' + container = 'quay.io/biocontainers/control-freec:11.5--he1b5a44_1' + shell = ['/bin/bash', '-euo', 'pipefail'] + + input: + tuple(sample_id, path(ratio_file), path(cnv_file)) + + output: + tuple(sample_id, path("${cnv_file.name}.p.value.txt"), emit: cnv_pvalue) + + script: + """ + cat /usr/local/bin/assess_significance.R | R --slave --args ${cnv_file} ${ratio_file} + """ +} diff --git a/ControlFREEC/11.5/Freec.nf b/ControlFREEC/11.5/Freec.nf new file mode 100644 index 00000000..aff81654 --- /dev/null +++ b/ControlFREEC/11.5/Freec.nf @@ -0,0 +1,19 @@ +process Freec { + tag {"Control Freec ${sample_id}"} + label 'ControlFreec_11_5' + label 'ControlFreec_11_5_Freec' + container = 'quay.io/biocontainers/control-freec:11.5--he1b5a44_1' + shell = ['/bin/bash', '-euo', 'pipefail'] + + input: + tuple(sample_id, path(bam_file), path(bai_file)) + + output: + tuple(sample_id, path("${bam_file.name}_ratio.txt"), path("${bam_file.name}_CNVs"), emit: cnv) + tuple(sample_id, path("${bam_file.name}_sample.cpn"), path("${bam_file.name}_ratio.BedGraph"), path("${bam_file.name}_info.txt"), emit: other) + + script: + """ + freec -conf ${params.config} -sample ${bam_file} + """ +} diff --git a/ControlFREEC/11.5/MakeGraph.nf b/ControlFREEC/11.5/MakeGraph.nf new file mode 100644 index 00000000..bde902f2 --- /dev/null +++ b/ControlFREEC/11.5/MakeGraph.nf @@ -0,0 +1,18 @@ +process MakeGraph { + tag {"Control Freec MakeGraph ${sample_id}"} + label 'ControlFreec_11_5' + label 'ControlFreec_11_5_MakeGraph' + container = 'quay.io/biocontainers/control-freec:11.5--he1b5a44_1' + shell = ['/bin/bash', '-euo', 'pipefail'] + + input: + tuple(sample_id, path(ratio_file), path(cnv_file)) + + output: + tuple(sample_id, path("${ratio_file.name}.png"), path("${ratio_file.name}.log2.png"), emit: ratio_png) + + script: + """ + cat /usr/local/bin/makeGraph.R | R --slave --args ${params.ploidy} ${ratio_file} + """ +} diff --git a/ControlFREEC/11.6/ControlFREEC.nf b/ControlFREEC/11.6/ControlFREEC.nf deleted file mode 100644 index d8e537ec..00000000 --- a/ControlFREEC/11.6/ControlFREEC.nf +++ /dev/null @@ -1,17 +0,0 @@ -process Freec { - tag {"Control_FREEC ${sample_id}"} - label 'Control_FREEC_11_6' - container = 'quay.io/biocontainers/control-freec:11.6--he1b5a44_0' - shell = ['/bin/bash', '-euo', 'pipefail'] - - input: - tuple(sample_id, path(bam_file), path(bai_file)) - - output: - tuple(sample_id, path("*")) - - script: - """ - freec -conf ${params.config} -sample ${bam_file} - """ -} From d9678efd191f640a9a49bd40f4c1edecfef7ae93 Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Thu, 11 Jun 2020 16:40:21 +0200 Subject: [PATCH 14/22] Create config in process --- ControlFREEC/11.5/Freec.nf | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/ControlFREEC/11.5/Freec.nf b/ControlFREEC/11.5/Freec.nf index aff81654..07992d2b 100644 --- a/ControlFREEC/11.5/Freec.nf +++ b/ControlFREEC/11.5/Freec.nf @@ -13,7 +13,22 @@ process Freec { tuple(sample_id, path("${bam_file.name}_sample.cpn"), path("${bam_file.name}_ratio.BedGraph"), path("${bam_file.name}_info.txt"), emit: other) script: + def config = '${sample_id}.config' """ - freec -conf ${params.config} -sample ${bam_file} + touch ${config} + echo "[general]" >> ${config} + echo "chrLenFile = ${params.chr_len_file}" >> ${config} + echo "chrFiles = ${params.chr_files}" >> ${config} + echo "gemMappabilityFile = ${params.gem_mappability_file}" >> ${config} + echo "ploidy = ${params.ploidy}" >> ${config} + echo "window = ${params.window}" >> ${config} + echo "BedGraphOutput=TRUE" >> ${config} + echo "maxThreads=${task.cpus}" >> ${config} + + echo "[sample]" >> ${config} + echo "inputFormat = BAM" >> ${config} + echo "mateFile = ${bam_file}" >> ${config} + + freec -conf ${config} """ } From ab68a08ffe048b4bc317acbd4e73e35e0668fff7 Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Fri, 12 Jun 2020 11:26:55 +0200 Subject: [PATCH 15/22] Fix config def --- ControlFREEC/11.5/Freec.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ControlFREEC/11.5/Freec.nf b/ControlFREEC/11.5/Freec.nf index 07992d2b..5aee35fe 100644 --- a/ControlFREEC/11.5/Freec.nf +++ b/ControlFREEC/11.5/Freec.nf @@ -13,7 +13,7 @@ process Freec { tuple(sample_id, path("${bam_file.name}_sample.cpn"), path("${bam_file.name}_ratio.BedGraph"), path("${bam_file.name}_info.txt"), emit: other) script: - def config = '${sample_id}.config' + def config = "${sample_id}.config" """ touch ${config} echo "[general]" >> ${config} From c782c51e35a8e7b661a0050a80a69ad5f76fb20f Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Fri, 12 Jun 2020 14:06:38 +0200 Subject: [PATCH 16/22] Add CollectWgsMetrics --- Picard/2.22.0/CollectWgsMetrics.nf | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 Picard/2.22.0/CollectWgsMetrics.nf diff --git a/Picard/2.22.0/CollectWgsMetrics.nf b/Picard/2.22.0/CollectWgsMetrics.nf new file mode 100644 index 00000000..5002aecd --- /dev/null +++ b/Picard/2.22.0/CollectWgsMetrics.nf @@ -0,0 +1,18 @@ +process CollectWgsMetrics { + tag {"PICARD CollectWgsMetrics ${sample_id}"} + label 'PICARD_2_22_0' + label 'PICARD_2_22_0_CollectWgsMetrics' + container = 'quay.io/biocontainers/picard:2.22.0--0' + shell = ['/bin/bash', '-euo', 'pipefail'] + + input: + tuple(sample_id, path(bam_file), path(bai_file)) + + output: + path("${sample_id}.WGSMetrics.txt", emit: txt_file) + + script: + """ + picard -Xmx${task.memory.toGiga()-4}G CollectWgsMetrics TMP_DIR=\$TMPDIR R=${params.genome} INPUT=${bam_file} OUTPUT=${sample_id}.WGSMetrics.txt ${params.optional} + """ +} From 77356725d04fcbf1a418f3331ddd20eb910f19e5 Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Mon, 15 Jun 2020 10:16:47 +0200 Subject: [PATCH 17/22] Multiqc compatibility --- Picard/2.22.0/CollectWgsMetrics.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Picard/2.22.0/CollectWgsMetrics.nf b/Picard/2.22.0/CollectWgsMetrics.nf index 5002aecd..d1679793 100644 --- a/Picard/2.22.0/CollectWgsMetrics.nf +++ b/Picard/2.22.0/CollectWgsMetrics.nf @@ -9,7 +9,7 @@ process CollectWgsMetrics { tuple(sample_id, path(bam_file), path(bai_file)) output: - path("${sample_id}.WGSMetrics.txt", emit: txt_file) + path("${sample_id}.wgs_metrics.txt", emit: txt_file) script: """ From c2af63360ec6bf23d09a641ef0985c2c13159bd7 Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Mon, 15 Jun 2020 10:17:00 +0200 Subject: [PATCH 18/22] Add MultiQC 1.9 --- MultiQC/1.9/MultiQC.nf | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 MultiQC/1.9/MultiQC.nf diff --git a/MultiQC/1.9/MultiQC.nf b/MultiQC/1.9/MultiQC.nf new file mode 100644 index 00000000..7b455ff8 --- /dev/null +++ b/MultiQC/1.9/MultiQC.nf @@ -0,0 +1,18 @@ +process MultiQC { + tag {"MultiQC"} + label 'MultiQC_1_9' + container = 'quay.io/biocontainers/multiqc:1.9--pyh9f0ad1d_0' + shell = ['/bin/bash', '-euo', 'pipefail'] + + input: + val(analysis_id) + path(qc_files) + + output: + tuple(path("${analysis_id}_multiqc_report.html"), path("${analysis_id}_multiqc_report_data"), emit: report) + + script: + """ + multiqc ${params.optional} --title ${analysis_id} . + """ +} From 1d22468da0a544db28f518148c0cc7a3acade4c7 Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Mon, 15 Jun 2020 12:26:20 +0200 Subject: [PATCH 19/22] Update to .gz files --- GATK/3.8-1-0-gf15c1c3ef/CatVariants.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/GATK/3.8-1-0-gf15c1c3ef/CatVariants.nf b/GATK/3.8-1-0-gf15c1c3ef/CatVariants.nf index fe5aa5e5..ca673c79 100644 --- a/GATK/3.8-1-0-gf15c1c3ef/CatVariants.nf +++ b/GATK/3.8-1-0-gf15c1c3ef/CatVariants.nf @@ -9,11 +9,11 @@ process CatVariantsGVCF { tuple(sample_id, path(gvcf_files), path(gvcf_idx_files)) output: - tuple(sample_id, path("${sample_id}.g.vcf"), path("${sample_id}.g.vcf.idx"), emit:vcf_file) + tuple(sample_id, path("${sample_id}.g.vcf.gz"), path("${sample_id}.g.vcf.gz.tbi"), emit:vcf_file) script: def input_files = gvcf_files.collect{"$it"}.join(" -V ") """ - java -Xmx${task.memory.toGiga()-4}G -cp ${params.gatk_path} org.broadinstitute.gatk.tools.CatVariants --reference ${params.genome} -V ${input_files} --outputFile ${sample_id}.g.vcf ${params.optional} + java -Xmx${task.memory.toGiga()-4}G -cp ${params.gatk_path} org.broadinstitute.gatk.tools.CatVariants --reference ${params.genome} -V ${input_files} --outputFile ${sample_id}.g.vcf.gz ${params.optional} """ } From fe1a6161fdaaa978775c3ff4e567bd6bab5b617d Mon Sep 17 00:00:00 2001 From: Robert Ernst Date: Mon, 15 Jun 2020 12:27:03 +0200 Subject: [PATCH 20/22] Rename output. --- Picard/2.22.0/CollectWgsMetrics.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Picard/2.22.0/CollectWgsMetrics.nf b/Picard/2.22.0/CollectWgsMetrics.nf index d1679793..66e51fb2 100644 --- a/Picard/2.22.0/CollectWgsMetrics.nf +++ b/Picard/2.22.0/CollectWgsMetrics.nf @@ -13,6 +13,6 @@ process CollectWgsMetrics { script: """ - picard -Xmx${task.memory.toGiga()-4}G CollectWgsMetrics TMP_DIR=\$TMPDIR R=${params.genome} INPUT=${bam_file} OUTPUT=${sample_id}.WGSMetrics.txt ${params.optional} + picard -Xmx${task.memory.toGiga()-4}G CollectWgsMetrics TMP_DIR=\$TMPDIR R=${params.genome} INPUT=${bam_file} OUTPUT=${sample_id}.wgs_metrics.txt ${params.optional} """ } From 5733f26ad6da26bebbcdcb3e0f0e04c13442b1b9 Mon Sep 17 00:00:00 2001 From: Sander Boymans Date: Tue, 16 Jun 2020 09:25:38 +0200 Subject: [PATCH 21/22] Added controlfreec & manta --- Control-FREEC/v11.5/ControlFreec.nf | 38 +++++++++++++++++++++++++++++ Manta/1.6.0/Manta.nf | 14 +++++------ 2 files changed, 45 insertions(+), 7 deletions(-) create mode 100644 Control-FREEC/v11.5/ControlFreec.nf diff --git a/Control-FREEC/v11.5/ControlFreec.nf b/Control-FREEC/v11.5/ControlFreec.nf new file mode 100644 index 00000000..43c7f3b8 --- /dev/null +++ b/Control-FREEC/v11.5/ControlFreec.nf @@ -0,0 +1,38 @@ +process ControlFreec { + tag {"ControlFreec ${sample_id}"} + label 'ControlFreec_11_5' + //label 'Tool_verion_Command' + container = '/hpc/cuppen/projects/TP0002_USEQ/general/analysis/sboymans/singularity/freec11.5.squashfs' + shell = ['/bin/bash', '-euo', 'pipefail'] + + input: + tuple(sample_id, path(bam_file),path(bai_file)) + + output: + tuple(sample_id, path("${config}"),path("${bam_file}_CNVs"),path("${bam_file}_ratio.txt"),path("${bam_file}_CNVs.p.value.txt"),path("${bam_file}_ratio.txt.log2.png"),path("${bam_file}_ratio.txt.png"),path("${bam_file}_ratio_karyotype.pdf"), emit: output_file) + + script: + config = "${sample_id}_freec.config" + """ + touch ${config} + echo "[general]" >> ${config} + echo "chrLenFile = ${params.genome_freec_chr_len}" >> ${config} + printf "${params.optional}" >> ${config} + echo "samtools = samtools" >> ${config} + echo "sambamba = sambamba" >> ${config} + echo "chrFiles = ${params.genome_freec_chr_files}" >> ${config} + echo "maxThreads = ${task.cpus}" >> ${config} + echo "outputDir = ." >> ${config} + echo "gemMappabilityFile = ${params.genome_freec_mappability}" >> ${config} + echo "[sample]" >> ${config} + echo "mateFile = ${bam_file}" >> ${config} + echo "inputFormat = BAM" >> ${config} + echo "mateOrientation = FR" >> ${config} + + freec -conf ${config} + + cat /bin/assess_significance.R | R --slave --args ${bam_file}_CNVs ${bam_file}_ratio.txt + cat /bin/makeGraph.R | R --slave --args 2 ${bam_file}_ratio.txt + cat /bin/makeKaryotype.R | R --slave --args 2 4 500000 ${bam_file}_ratio.txt + """ +} diff --git a/Manta/1.6.0/Manta.nf b/Manta/1.6.0/Manta.nf index 2d1b82c2..e7e34d6f 100644 --- a/Manta/1.6.0/Manta.nf +++ b/Manta/1.6.0/Manta.nf @@ -14,13 +14,13 @@ process Manta { script: """ ${params.manta_path}/configManta.py --referenceFasta ${params.genome_fasta} --runDir . --bam $bam_file - ${params.manta_path}/runWorkflow.py -m local -j ${task.cpus} + ./runWorkflow.py -m local -j ${task.cpus} - mv Manta/results/variants/candidateSmallIndels.vcf.gz Manta_${sample_id}.candidateSmallIndels.vcf.gz - mv Manta/results/variants/candidateSmallIndels.vcf.gz.tbi Manta_${sample_id}.candidateSmallIndels.vcf.gz.tbi - mv Manta/results/variants/candidateSV.vcf.gz Manta_${sample_id}.candidateSV.vcf.gz - mv Manta/results/variants/candidateSV.vcf.gz.tbi Manta_${sample_id}.candidateSV.vcf.gz.tbi - mv Manta/results/variants/diploidSV.vcf.gz Manta_${sample_id}.diploidSV.vcf.gz - mv Manta/results/variants/diploidSVSV.vcf.gz.tbi Manta_${sample_id}.diploidSV.vcf.gz.tbi + mv results/variants/candidateSmallIndels.vcf.gz Manta_${sample_id}.candidateSmallIndels.vcf.gz + mv results/variants/candidateSmallIndels.vcf.gz.tbi Manta_${sample_id}.candidateSmallIndels.vcf.gz.tbi + mv results/variants/candidateSV.vcf.gz Manta_${sample_id}.candidateSV.vcf.gz + mv results/variants/candidateSV.vcf.gz.tbi Manta_${sample_id}.candidateSV.vcf.gz.tbi + mv results/variants/diploidSV.vcf.gz Manta_${sample_id}.diploidSV.vcf.gz + mv results/variants/diploidSV.vcf.gz.tbi Manta_${sample_id}.diploidSV.vcf.gz.tbi """ } From 1a3439a993b6dcd1dcc52c7ccaceccdb1fb6dbc8 Mon Sep 17 00:00:00 2001 From: Sander Boymans Date: Fri, 19 Jun 2020 10:18:44 +0200 Subject: [PATCH 22/22] Merged Robert's ControlFREEC modules, deleted old ones. Added Manta. Added containers for both manta & freec. --- Control-FREEC/v11.5/ControlFreec.nf | 38 ------------------------- ControlFREEC/11.5/AssessSignificance.nf | 4 +-- ControlFREEC/11.5/Freec.nf | 4 ++- ControlFREEC/11.5/MakeGraph.nf | 4 +-- ControlFREEC/11.5/MakeKaryotype.nf | 18 ++++++++++++ Manta/1.6.0/Manta.nf | 6 ++-- 6 files changed, 28 insertions(+), 46 deletions(-) delete mode 100644 Control-FREEC/v11.5/ControlFreec.nf create mode 100644 ControlFREEC/11.5/MakeKaryotype.nf diff --git a/Control-FREEC/v11.5/ControlFreec.nf b/Control-FREEC/v11.5/ControlFreec.nf deleted file mode 100644 index 43c7f3b8..00000000 --- a/Control-FREEC/v11.5/ControlFreec.nf +++ /dev/null @@ -1,38 +0,0 @@ -process ControlFreec { - tag {"ControlFreec ${sample_id}"} - label 'ControlFreec_11_5' - //label 'Tool_verion_Command' - container = '/hpc/cuppen/projects/TP0002_USEQ/general/analysis/sboymans/singularity/freec11.5.squashfs' - shell = ['/bin/bash', '-euo', 'pipefail'] - - input: - tuple(sample_id, path(bam_file),path(bai_file)) - - output: - tuple(sample_id, path("${config}"),path("${bam_file}_CNVs"),path("${bam_file}_ratio.txt"),path("${bam_file}_CNVs.p.value.txt"),path("${bam_file}_ratio.txt.log2.png"),path("${bam_file}_ratio.txt.png"),path("${bam_file}_ratio_karyotype.pdf"), emit: output_file) - - script: - config = "${sample_id}_freec.config" - """ - touch ${config} - echo "[general]" >> ${config} - echo "chrLenFile = ${params.genome_freec_chr_len}" >> ${config} - printf "${params.optional}" >> ${config} - echo "samtools = samtools" >> ${config} - echo "sambamba = sambamba" >> ${config} - echo "chrFiles = ${params.genome_freec_chr_files}" >> ${config} - echo "maxThreads = ${task.cpus}" >> ${config} - echo "outputDir = ." >> ${config} - echo "gemMappabilityFile = ${params.genome_freec_mappability}" >> ${config} - echo "[sample]" >> ${config} - echo "mateFile = ${bam_file}" >> ${config} - echo "inputFormat = BAM" >> ${config} - echo "mateOrientation = FR" >> ${config} - - freec -conf ${config} - - cat /bin/assess_significance.R | R --slave --args ${bam_file}_CNVs ${bam_file}_ratio.txt - cat /bin/makeGraph.R | R --slave --args 2 ${bam_file}_ratio.txt - cat /bin/makeKaryotype.R | R --slave --args 2 4 500000 ${bam_file}_ratio.txt - """ -} diff --git a/ControlFREEC/11.5/AssessSignificance.nf b/ControlFREEC/11.5/AssessSignificance.nf index da0f9392..d4ce7af5 100644 --- a/ControlFREEC/11.5/AssessSignificance.nf +++ b/ControlFREEC/11.5/AssessSignificance.nf @@ -2,7 +2,7 @@ process AssessSignificance { tag {"Control Freec AssessSignificance ${sample_id}"} label 'ControlFreec_11_5' label 'ControlFreec_11_5_AssessSignificance' - container = 'quay.io/biocontainers/control-freec:11.5--he1b5a44_1' + container = 'library://sawibo/default/bioinf-tools:freec11.5' shell = ['/bin/bash', '-euo', 'pipefail'] input: @@ -13,6 +13,6 @@ process AssessSignificance { script: """ - cat /usr/local/bin/assess_significance.R | R --slave --args ${cnv_file} ${ratio_file} + cat /bin/assess_significance.R | R --slave --args ${cnv_file} ${ratio_file} """ } diff --git a/ControlFREEC/11.5/Freec.nf b/ControlFREEC/11.5/Freec.nf index 5aee35fe..c9422fcc 100644 --- a/ControlFREEC/11.5/Freec.nf +++ b/ControlFREEC/11.5/Freec.nf @@ -2,7 +2,8 @@ process Freec { tag {"Control Freec ${sample_id}"} label 'ControlFreec_11_5' label 'ControlFreec_11_5_Freec' - container = 'quay.io/biocontainers/control-freec:11.5--he1b5a44_1' + //TODO: upload to singularity library + container = 'library://sawibo/default/bioinf-tools:freec11.5' shell = ['/bin/bash', '-euo', 'pipefail'] input: @@ -22,6 +23,7 @@ process Freec { echo "gemMappabilityFile = ${params.gem_mappability_file}" >> ${config} echo "ploidy = ${params.ploidy}" >> ${config} echo "window = ${params.window}" >> ${config} + echo "telocentromeric = ${params.telocentromeric}" >> ${config} echo "BedGraphOutput=TRUE" >> ${config} echo "maxThreads=${task.cpus}" >> ${config} diff --git a/ControlFREEC/11.5/MakeGraph.nf b/ControlFREEC/11.5/MakeGraph.nf index bde902f2..3375d31b 100644 --- a/ControlFREEC/11.5/MakeGraph.nf +++ b/ControlFREEC/11.5/MakeGraph.nf @@ -2,7 +2,7 @@ process MakeGraph { tag {"Control Freec MakeGraph ${sample_id}"} label 'ControlFreec_11_5' label 'ControlFreec_11_5_MakeGraph' - container = 'quay.io/biocontainers/control-freec:11.5--he1b5a44_1' + container = 'library://sawibo/default/bioinf-tools:freec11.5' shell = ['/bin/bash', '-euo', 'pipefail'] input: @@ -13,6 +13,6 @@ process MakeGraph { script: """ - cat /usr/local/bin/makeGraph.R | R --slave --args ${params.ploidy} ${ratio_file} + cat /bin/makeGraph.R | R --slave --args ${params.ploidy} ${ratio_file} """ } diff --git a/ControlFREEC/11.5/MakeKaryotype.nf b/ControlFREEC/11.5/MakeKaryotype.nf new file mode 100644 index 00000000..a903e8d2 --- /dev/null +++ b/ControlFREEC/11.5/MakeKaryotype.nf @@ -0,0 +1,18 @@ +process MakeKaryotype { + tag {"Control Freec MakeKaryotype ${sample_id}"} + label 'ControlFreec_11_5' + label 'ControlFreec_11_5_MakeKaryotype' + container = 'library://sawibo/default/bioinf-tools:freec11.5' + shell = ['/bin/bash', '-euo', 'pipefail'] + + input: + tuple(sample_id, path(ratio_file), path(cnv_file)) + + output: + tuple(sample_id, path("*_karyotype.pdf"), emit: karyotype_pdf) + + script: + """ + cat /bin/makeKaryotype.R | R --slave --args ${params.ploidy} ${params.maxlevel} ${params.telocentromeric} ${ratio_file} + """ +} diff --git a/Manta/1.6.0/Manta.nf b/Manta/1.6.0/Manta.nf index e7e34d6f..cb7f7f70 100644 --- a/Manta/1.6.0/Manta.nf +++ b/Manta/1.6.0/Manta.nf @@ -2,18 +2,18 @@ process Manta { tag {"Manta ConfigAndRun ${sample_id}"} label 'Manta_1_6_0' label 'Manta_1_6_0_ConfigAndRun' - //container = 'container_url' + container = 'quay.io/biocontainers/manta:1.6.0--py27_0' shell = ['/bin/bash', '-euo', 'pipefail'] input: tuple (sample_id, path(bam_file), path(bai_file)) output: - tuple (sample_id, path("*.candidateSmallIndels.*"),path("*.candidateSV.*"),path("*.diploidSV.*"), emit: manta_vcfs ) + tuple (sample_id, path("*.candidateSmallIndels.*"),path("*.candidateSV.*"),path("*.diploidSV.*"), emit: sv ) script: """ - ${params.manta_path}/configManta.py --referenceFasta ${params.genome_fasta} --runDir . --bam $bam_file + configManta.py --referenceFasta ${params.genome_fasta} --runDir . --bam $bam_file ./runWorkflow.py -m local -j ${task.cpus} mv results/variants/candidateSmallIndels.vcf.gz Manta_${sample_id}.candidateSmallIndels.vcf.gz