Add config option to manta modules (nf-core#3890)

* new module picard/scatterintervalsbyns * update annotsv to 3.3.6 * update installannotations * add config to manta modules * fix mv somatic * add config tests
lrauschning · Oct 16, 2023 · 9a0ae7a · 9a0ae7a
1 parent d3dcfc7
commit 9a0ae7a
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Showing 9 changed files with 170 additions and 56 deletions.
diff --git a/modules/nf-core/manta/germline/main.nf b/modules/nf-core/manta/germline/main.nf
@@ -13,6 +13,7 @@ process MANTA_GERMLINE {
     tuple val(meta), path(input), path(index), path(target_bed), path(target_bed_tbi)
     tuple val(meta2), path(fasta)
     tuple val(meta3), path(fai)
+    path(config)
 
     output:
     tuple val(meta), path("*candidate_small_indels.vcf.gz")    , emit: candidate_small_indels_vcf
@@ -31,27 +32,29 @@ process MANTA_GERMLINE {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def input_files = input.collect{"--bam ${it}"}.join(' ')
     def options_manta = target_bed ? "--callRegions $target_bed" : ""
+    def config_option = config ? "--config ${config}" : ""
     """
-    configManta.py \
-        ${input_files} \
-        --reference $fasta \
-        --runDir manta \
-        $options_manta \
+    configManta.py \\
+        ${input_files} \\
+        ${config_option} \\
+        --reference $fasta \\
+        --runDir manta \\
+        $options_manta \\
         $args
 
     python manta/runWorkflow.py -m local -j $task.cpus
 
-    mv manta/results/variants/candidateSmallIndels.vcf.gz \
+    mv manta/results/variants/candidateSmallIndels.vcf.gz \\
         ${prefix}.candidate_small_indels.vcf.gz
-    mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi \
+    mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi \\
         ${prefix}.candidate_small_indels.vcf.gz.tbi
-    mv manta/results/variants/candidateSV.vcf.gz \
+    mv manta/results/variants/candidateSV.vcf.gz \\
         ${prefix}.candidate_sv.vcf.gz
-    mv manta/results/variants/candidateSV.vcf.gz.tbi \
+    mv manta/results/variants/candidateSV.vcf.gz.tbi \\
         ${prefix}.candidate_sv.vcf.gz.tbi
-    mv manta/results/variants/diploidSV.vcf.gz \
+    mv manta/results/variants/diploidSV.vcf.gz \\
         ${prefix}.diploid_sv.vcf.gz
-    mv manta/results/variants/diploidSV.vcf.gz.tbi \
+    mv manta/results/variants/diploidSV.vcf.gz.tbi \\
         ${prefix}.diploid_sv.vcf.gz.tbi
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/nf-core/manta/germline/meta.yml b/modules/nf-core/manta/germline/meta.yml
@@ -57,6 +57,10 @@ input:
       type: file
       description: Genome reference FASTA index file
       pattern: "*.{fa.fai,fasta.fai}"
+  - config:
+      type: file
+      description: Manta configuration file
+      pattern: "*.{ini,conf,config}"
 
 output:
   - meta:
@@ -96,3 +100,4 @@ output:
 authors:
   - "@maxulysse"
   - "@ramprasadn"
+  - "@nvnieuwk"
diff --git a/modules/nf-core/manta/somatic/main.nf b/modules/nf-core/manta/somatic/main.nf
@@ -10,8 +10,9 @@ process MANTA_SOMATIC {
 
     input:
     tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(target_bed), path(target_bed_tbi)
-    path fasta
-    path fai
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+    path(config)
 
     output:
     tuple val(meta), path("*.candidate_small_indels.vcf.gz")     , emit: candidate_small_indels_vcf
@@ -31,26 +32,53 @@ process MANTA_SOMATIC {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def options_manta = target_bed ? "--callRegions $target_bed" : ""
-
+    def config_option = config ? "--config ${config}" : ""
     """
-    configManta.py \
-        --tumorBam $input_tumor \
-        --normalBam $input_normal \
-        --reference $fasta \
-        --runDir manta \
-        $options_manta \
+    configManta.py \\
+        --tumorBam $input_tumor \\
+        --normalBam $input_normal \\
+        --reference $fasta \\
+        ${config_option} \\
+        --runDir manta \\
+        $options_manta \\
         $args
 
     python manta/runWorkflow.py -m local -j $task.cpus
 
-    mv manta/results/variants/candidateSmallIndels.vcf.gz     ${prefix}.candidate_small_indels.vcf.gz
-    mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi ${prefix}.candidate_small_indels.vcf.gz.tbi
-    mv manta/results/variants/candidateSV.vcf.gz              ${prefix}.candidate_sv.vcf.gz
-    mv manta/results/variants/candidateSV.vcf.gz.tbi          ${prefix}.candidate_sv.vcf.gz.tbi
-    mv manta/results/variants/diploidSV.vcf.gz                ${prefix}.diploid_sv.vcf.gz
-    mv manta/results/variants/diploidSV.vcf.gz.tbi            ${prefix}.diploid_sv.vcf.gz.tbi
-    mv manta/results/variants/somaticSV.vcf.gz                ${prefix}.somatic_sv.vcf.gz
-    mv manta/results/variants/somaticSV.vcf.gz.tbi            ${prefix}.somatic_sv.vcf.gz.tbi
+    mv manta/results/variants/candidateSmallIndels.vcf.gz \\
+        ${prefix}.candidate_small_indels.vcf.gz
+    mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi \\
+        ${prefix}.candidate_small_indels.vcf.gz.tbi
+    mv manta/results/variants/candidateSV.vcf.gz \\
+        ${prefix}.candidate_sv.vcf.gz
+    mv manta/results/variants/candidateSV.vcf.gz.tbi \\
+        ${prefix}.candidate_sv.vcf.gz.tbi
+    mv manta/results/variants/diploidSV.vcf.gz \\
+        ${prefix}.diploid_sv.vcf.gz
+    mv manta/results/variants/diploidSV.vcf.gz.tbi \\
+        ${prefix}.diploid_sv.vcf.gz.tbi
+    mv manta/results/variants/somaticSV.vcf.gz \\
+        ${prefix}.somatic_sv.vcf.gz
+    mv manta/results/variants/somaticSV.vcf.gz.tbi \\
+        ${prefix}.somatic_sv.vcf.gz.tbi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        manta: \$( configManta.py --version )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.candidate_small_indels.vcf.gz
+    touch ${prefix}.candidate_small_indels.vcf.gz.tbi
+    touch ${prefix}.candidate_sv.vcf.gz
+    touch ${prefix}.candidate_sv.vcf.gz.tbi
+    touch ${prefix}.diploid_sv.vcf.gz
+    touch ${prefix}.diploid_sv.vcf.gz.tbi
+    touch ${prefix}.somatic_sv.vcf.gz
+    touch ${prefix}.somatic_sv.vcf.gz.tbi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/manta/somatic/meta.yml b/modules/nf-core/manta/somatic/meta.yml
@@ -47,14 +47,28 @@ input:
       type: file
       description: Index for BED file containing target regions for variant calling
       pattern: "*.{bed.tbi}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
   - fasta:
       type: file
       description: Genome reference FASTA file
       pattern: "*.{fa,fasta}"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
   - fai:
       type: file
       description: Genome reference FASTA index file
       pattern: "*.{fa.fai,fasta.fai}"
+  - config:
+      type: file
+      description: Manta configuration file
+      pattern: "*.{ini,conf,config}"
 
 output:
   - meta:
@@ -101,3 +115,4 @@ output:
 
 authors:
   - "@FriederikeHanssen"
+  - "@nvnieuwk"
diff --git a/modules/nf-core/manta/tumoronly/main.nf b/modules/nf-core/manta/tumoronly/main.nf
@@ -10,8 +10,9 @@ process MANTA_TUMORONLY {
 
     input:
     tuple val(meta), path(input), path(input_index), path(target_bed), path(target_bed_tbi)
-    path fasta
-    path fai
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+    path(config)
 
     output:
     tuple val(meta), path("*candidate_small_indels.vcf.gz")    , emit: candidate_small_indels_vcf
@@ -29,32 +30,50 @@ process MANTA_TUMORONLY {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def options_manta = target_bed ? "--callRegions $target_bed" : ""
+    def config_option = config ? "--config ${config}" : ""
     """
-    configManta.py \
-        --tumorBam $input \
-        --reference $fasta \
-        --runDir manta \
-        $options_manta \
+    configManta.py \\
+        --tumorBam $input \\
+        --reference $fasta \\
+        ${config_option} \\
+        --runDir manta \\
+        $options_manta \\
         $args
 
     python manta/runWorkflow.py -m local -j $task.cpus
 
-    mv manta/results/variants/candidateSmallIndels.vcf.gz \
+    mv manta/results/variants/candidateSmallIndels.vcf.gz \\
         ${prefix}.candidate_small_indels.vcf.gz
-    mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi \
+    mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi \\
         ${prefix}.candidate_small_indels.vcf.gz.tbi
-    mv manta/results/variants/candidateSV.vcf.gz \
+    mv manta/results/variants/candidateSV.vcf.gz \\
         ${prefix}.candidate_sv.vcf.gz
-    mv manta/results/variants/candidateSV.vcf.gz.tbi \
+    mv manta/results/variants/candidateSV.vcf.gz.tbi \\
         ${prefix}.candidate_sv.vcf.gz.tbi
-    mv manta/results/variants/tumorSV.vcf.gz \
+    mv manta/results/variants/tumorSV.vcf.gz \\
         ${prefix}.tumor_sv.vcf.gz
-    mv manta/results/variants/tumorSV.vcf.gz.tbi \
+    mv manta/results/variants/tumorSV.vcf.gz.tbi \\
         ${prefix}.tumor_sv.vcf.gz.tbi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         manta: \$( configManta.py --version )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.candidate_small_indels.vcf.gz
+    touch ${prefix}.candidate_small_indels.vcf.gz.tbi
+    touch ${prefix}.candidate_sv.vcf.gz
+    touch ${prefix}.candidate_sv.vcf.gz.tbi
+    touch ${prefix}.tumor_sv.vcf.gz
+    touch ${prefix}.tumor_sv.vcf.gz.tbi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        manta: \$( configManta.py --version )
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/manta/tumoronly/meta.yml b/modules/nf-core/manta/tumoronly/meta.yml
@@ -39,14 +39,28 @@ input:
       type: file
       description: Index for BED file containing target regions for variant calling
       pattern: "*.{bed.tbi}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
   - fasta:
       type: file
       description: Genome reference FASTA file
       pattern: "*.{fa,fasta}"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
   - fai:
       type: file
       description: Genome reference FASTA index file
       pattern: "*.{fa.fai,fasta.fai}"
+  - config:
+      type: file
+      description: Manta configuration file
+      pattern: "*.{ini,conf,config}"
 
 output:
   - meta:
@@ -85,3 +99,4 @@ output:
 
 authors:
   - "@maxulysse"
+  - "@nvnieuwk"
diff --git a/tests/modules/nf-core/manta/germline/main.nf b/tests/modules/nf-core/manta/germline/main.nf
@@ -18,7 +18,10 @@ workflow test_manta_germline {
               file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
             ]
 
-    MANTA_GERMLINE ( input, fasta, fai )
+    config = Channel.of("[manta]", "enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = 0")
+        .collectFile(name:"manta_options.ini", newLine:true)
+
+    MANTA_GERMLINE ( input, fasta, fai, config )
 }
 
 workflow test_manta_germline_target_bed {
@@ -36,7 +39,7 @@ workflow test_manta_germline_target_bed {
               file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
             ]
 
-    MANTA_GERMLINE ( input, fasta, fai )
+    MANTA_GERMLINE ( input, fasta, fai, [] )
 }
 
 workflow test_manta_germline_target_bed_jointcalling {
@@ -56,5 +59,5 @@ workflow test_manta_germline_target_bed_jointcalling {
               file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
             ]
 
-    MANTA_GERMLINE ( input, fasta, fai )
+    MANTA_GERMLINE ( input, fasta, fai, [] )
 }
diff --git a/tests/modules/nf-core/manta/somatic/main.nf b/tests/modules/nf-core/manta/somatic/main.nf
@@ -15,10 +15,18 @@ workflow test_manta_somatic {
         [], []
     ]
 
-    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    fasta = [ [id:'genome'],
+              file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+            ]
 
-    MANTA_SOMATIC ( input, fasta, fai )
+    fai   = [ [id:'genome'],
+              file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+            ]
+
+    config = Channel.of("[manta]", "enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = 0")
+        .collectFile(name:"manta_options.ini", newLine:true)
+
+    MANTA_SOMATIC ( input, fasta, fai, config )
 }
 
 workflow test_manta_somatic_target_bed {
@@ -33,8 +41,13 @@ workflow test_manta_somatic_target_bed {
         file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true),
     ]
 
-    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    fasta = [ [id:'genome'],
+              file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+            ]
+
+    fai   = [ [id:'genome'],
+              file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+            ]
 
-    MANTA_SOMATIC ( input, fasta, fai )
+    MANTA_SOMATIC ( input, fasta, fai, [] )
 }
diff --git a/tests/modules/nf-core/manta/tumoronly/main.nf b/tests/modules/nf-core/manta/tumoronly/main.nf
@@ -12,10 +12,18 @@ workflow test_manta_tumoronly {
         [], []
     ]
 
-    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    fasta = [ [id:'genome'],
+              file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+            ]
 
-    MANTA_TUMORONLY ( input, fasta, fai )
+    fai   = [ [id:'genome'],
+              file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+            ]
+
+    config = Channel.of("[manta]", "enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = 0")
+        .collectFile(name:"manta_options.ini", newLine:true)
+
+    MANTA_TUMORONLY ( input, fasta, fai, config )
 }
 
 workflow test_manta_tumoronly_target_bed {
@@ -27,8 +35,13 @@ workflow test_manta_tumoronly_target_bed {
         file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true)
     ]
 
-    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    fasta = [ [id:'genome'],
+              file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+            ]
+
+    fai   = [ [id:'genome'],
+              file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+            ]
 
-    MANTA_TUMORONLY ( input, fasta, fai )
+    MANTA_TUMORONLY ( input, fasta, fai, [] )
 }