fix: gs10 data partition; container syntax; input file name collision in Octopus; AnnotSV missing db; name tag

CHANGELOG.md

@@ -1,5 +1,9 @@
 ## LOGAN development version
 
+- Fixed container mount error - removed broken paths. (#111, @samarth8392)
+- Fixed input file name collision in Octopus variant calling. (#111, @samarth8392)
+- Fixed AnnotSV database path resolution in tumor-only SV workflows. (#111, @samarth8392)
+
 ## LOGAN 0.3.2
 
 - Uses Nextflow v25 for logan run; fixes the bug in stub run in nf v24.10 (see: https://github.com/nextflow-io/nextflow/issues/5456) (#99, @samarth8392)

conf/biowulf.config

@@ -22,6 +22,7 @@ singularity {
     autoMounts = true
     cacheDir = "/data/CCBR_Pipeliner/SIFS"
     envWhitelist = 'https_proxy,http_proxy,ftp_proxy,DISPLAY,SLURM_JOBID,SINGULARITY_BINDPATH'
+    runOptions = '-B /data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/AnnotSV:/annotsv_db'
 }
 
 env.SINGULARITY_CACHEDIR = "/data/CCBR_Pipeliner/SIFS"

conf/ci_stub.config

@@ -17,7 +17,7 @@ singularity {
     autoMounts = true
     cacheDir = "/data/CCBR_Pipeliner/SIFS"
     envWhitelist = 'https_proxy,http_proxy,ftp_proxy,DISPLAY,SLURM_JOBID,SINGULARITY_BINDPATH'
-    runOptions = '-B /gs10,/gs11,/gs12,/spin1,/data/CCBR_Pipeliner/,/vf/users,/gpfs,/fdb'
+    runOptions = '-B /data/CCBR_Pipeliner/,/vf/users,/gpfs,/fdb'
 }
 
 env.SINGULARITY_CACHEDIR = "/data/CCBR_Pipeliner/SIFS"

conf/genomes.config

@@ -26,6 +26,7 @@ params {
             vepspecies = "homo_sapiens"
             vepbuild = "GRCh38"
             annotsvgenome = "GRCh38"
+            annotsvdb = "/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/AnnotSV"
             octopus_sforest= "--somatic-forest /data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/octopus/somatic.v0.7.4.forest"
             octopus_gforest= "--forest /data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/octopus/germline.v0.7.4.forest"
             SEQUENZAGC = "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/SEQUENZA/hg38.gc200Base.wig.gz"
@@ -185,6 +186,7 @@ params {
             vepspecies = "homo_sapiens"
             vepbuild = "GRCh38"
             annotsvgenome = "GRCh38"
+            annotsvdb = "/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/AnnotSV"
             octopus_sforest= "--somatic-forest /data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/octopus/somatic.v0.7.4.forest"
             octopus_gforest= "--forest /data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/octopus/germline.v0.7.4.forest"
             SEQUENZAGC = "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/SEQUENZA/hg38.gc200Base.wig.gz"
@@ -240,6 +242,7 @@ params {
             vepspecies = "homo_sapiens"
             vepbuild = "GRCh38"
             annotsvgenome = "GRCh38"
+            annotsvdb = "/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/AnnotSV"
             octopus_sforest= "--somatic-forest /data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/octopus/somatic.v0.7.4.forest"
             octopus_gforest= "--forest /data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/octopus/germline.v0.7.4.forest"
             SEQUENZAGC = "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/SEQUENZA/hg38.gc200Base.wig.gz"

modules/local/annotsv.nf

@@ -1,12 +1,10 @@
 GENOMEREF=file(params.genomes[params.genome].genome)
-ANNOTSVGENOME=params.genomes[params.genome].annotsvgenome
-
 
 process annotsv_tn {
-     //AnnotSV for Manta/Svaba/GRIDSS works with either vcf.gz or .vcf files
-     //Requires bedtools,bcftools
+    //AnnotSV for Manta/Svaba/GRIDSS works with either vcf.gz or .vcf files
+    //Requires bedtools,bcftools
     errorStrategy = 'ignore'
-    container = "${params.containers.annotcnvsv}"
+    container "${params.containers.annotcnvsv}"
 
     input:
         tuple val(tumorname), path(somaticvcf), val(sv)
@@ -16,91 +14,82 @@ process annotsv_tn {
         path("${sv}/${tumorname}.tsv"),
         path("${sv}/${tumorname}.unannotated.tsv")
 
-
     script:
+    def annotsvGenome = params.genomes[params.genome].annotsvgenome
     """
     mkdir ${sv}
 
     AnnotSV -SVinputFile ${somaticvcf} \
-    -genomeBuild $ANNOTSVGENOME \
+    -genomeBuild ${annotsvGenome} \
+    -annotationsDir /annotsv_db \
     -SVinputInfo 1 -outputFile ${tumorname} \
     -outputDir ${sv}
 
+    # Create empty files if AnnotSV didn't produce output (empty VCF)
+    touch ${sv}/${tumorname}.tsv
+    touch ${sv}/${tumorname}.unannotated.tsv
     """
 
     stub:
     """
     mkdir ${sv}
-
     touch "${sv}/${tumorname}.tsv"
     touch "${sv}/${tumorname}.unannotated.tsv"
     """
 }
 
-
-
-
 process gunzip {
     label 'process_single'
 
     input:
-        tuple val(tumorname),
-        path(vcf), val(sv)
+        tuple val(tumorname), path(vcf), val(sv)
 
     output:
         tuple val(tumorname),
         path("${tumorname}.tumorSV_${sv}.vcf"), val(sv)
 
     script:
     """
-    gunzip -f ${vcf} > ${tumorname}.tumorSV_${sv}.vcf
+    gunzip -c ${vcf} > ${tumorname}.tumorSV_${sv}.vcf
     """
 
     stub:
-
     """
     touch ${tumorname}.tumorSV_${sv}.vcf
     """
-
 }
 
-
 process survivor_sv {
-    container = "${params.containers.annotcnvsv}"
+    container "${params.containers.annotcnvsv}"
 
     input:
-        tuple val(tumorname),
-        path(vcfs), val(svs)
+        tuple val(tumorname), path(vcfs), val(svs)
 
     output:
         tuple val(tumorname),
         path("${tumorname}_merged.vcf"),
         val("survivor")
 
-
     script:
-    strin = vcfs.join("\\n")
-
+    def strin = vcfs.join("\\n")
     """
-    echo -e '$strin' > filelistin
+    echo -e '${strin}' > filelistin
     SURVIVOR merge filelistin 1000 2 1 1 1 30 ${tumorname}_merged.vcf
     """
 
     stub:
-    strin = vcfs.join("\\n")
+    def strin = vcfs.join("\\n")
     """
-    echo -e '$strin' > filelistin
+    echo -e '${strin}' > filelistin
     touch "${tumorname}_merged.vcf"
     """
 }
 
-
 process annotsv_tonly {
-     //AnnotSV for Manta/Svaba works with either vcf.gz or .vcf files
-     //Requires bedtools,bcftools
+    //AnnotSV for Manta/Svaba works with either vcf.gz or .vcf files
+    //Requires bedtools,bcftools
     errorStrategy = 'ignore'
-
-    container = "${params.containers.annotcnvsv}"
+    container "${params.containers.annotcnvsv}"
 
     input:
         tuple val(tumorname), path(somaticvcf), val(sv)
@@ -110,23 +99,26 @@ process annotsv_tonly {
         path("${sv}/${tumorname}.tsv"),
         path("${sv}/${tumorname}.unannotated.tsv")
 
-
     script:
+    def annotsvGenome = params.genomes[params.genome].annotsvgenome
     """
     mkdir ${sv}
 
     AnnotSV -SVinputFile ${somaticvcf} \
-    -genomeBuild $ANNOTSVGENOME \
+    -genomeBuild ${annotsvGenome} \
+    -annotationsDir /annotsv_db \
     -SVinputInfo 1 -outputFile ${tumorname} \
     -outputDir ${sv}
 
+    # Create empty files if AnnotSV didn't produce output (empty VCF)
+    touch ${sv}/${tumorname}.tsv
+    touch ${sv}/${tumorname}.unannotated.tsv
     """
 
     stub:
     """
     mkdir ${sv}
-
     touch "${sv}/${tumorname}.tsv"
     touch "${sv}/${tumorname}.unannotated.tsv"
     """
-}
+}

modules/local/ascat.nf

@@ -7,7 +7,7 @@ if (params.genome.matches("hg38(.*)")){
 
 
 process ascat_tn {
-    container = "${params.containers.cnv}"
+    container "${params.containers.cnv}"
     label 'process_medium'
 
     input:
@@ -57,7 +57,7 @@ process ascat_tn {
 
 
 process ascat_tn_exome {
-    container = "${params.containers.cnv}"
+    container "${params.containers.cnv}"
     label 'process_medium'
 
     input:

modules/local/bcftools_stats.nf

@@ -12,7 +12,7 @@ process bcftools_stats {
     @Output:
         Text file containing a collection of summary statistics
     */
-    container = "${params.containers.logan}"
+    container "${params.containers.logan}"
     label 'process_medium'
 
     input:

modules/local/bwamem/bwamem2.nf

@@ -1,8 +1,8 @@
 GENOMEREF = file(params.genomes[params.genome].genome)
 
 process bwamem2 {
-    container = "${params.containers.logan}"
-    tag { name }
+    container "${params.containers.logan}"
+    tag { samplename }
     errorStrategy { task.exitStatus in [137,140,143] ? 'retry' : 'terminate' }
     maxRetries 2
 
@@ -53,7 +53,7 @@ process bwamem2 {
 
 
 process BWAMEM2_SPLIT {
-    container = "${params.containers.logan}"
+    container "${params.containers.logan}"
     tag { name }
     errorStrategy { task.exitStatus in [137,140,143] ? 'retry' : 'terminate' }
     maxRetries 2
@@ -105,7 +105,7 @@ process BWAMEM2_SPLIT {
 
 
 process COMBINE_ALIGNMENTS {
-    container = "${params.containers.logan}"
+    container "${params.containers.logan}"
     label 'process_medium'
 
     input:

modules/local/cnvkit.nf

@@ -7,7 +7,7 @@ REFFLAT = file(params.genomes[params.genome].REFFLAT)
 ACCESS = file(params.genomes[params.genome].ACCESS)
 
 process cnvkit {
-    container = "${params.containers.cnv}"
+    container "${params.containers.cnv}"
     label 'process_medium'
 
     input:
@@ -40,7 +40,7 @@ process cnvkit {
 }
 
 process cnvkit_exome {
-    container = "${params.containers.cnv}"
+    container "${params.containers.cnv}"
     label 'process_medium'
 
     input:
@@ -74,7 +74,7 @@ process cnvkit_exome {
 
 
 process cnvkit_tonly {
-    container = "${params.containers.cnv}"
+    container "${params.containers.cnv}"
     label 'process_medium'
 
     input:
@@ -104,7 +104,7 @@ process cnvkit_tonly {
 }
 
 process cnvkit_exome_tonly {
-    container = "${params.containers.cnv}"
+    container "${params.containers.cnv}"
     label 'process_medium'
 
     input:

modules/local/deepsomatic.nf

@@ -11,7 +11,7 @@ if(params.exome && params.ffpe) {
 }
 
 process deepsomatic_tn_step1 {
-    container = "${params.containers.deepsomatic}"
+    container "${params.containers.deepsomatic}"
     label 'process_somaticcaller'
     errorStrategy { task.exitStatus == 1 ? 'ignore' : 'terminate' }
 
@@ -52,7 +52,7 @@ process deepsomatic_tn_step1 {
 
 
 process deepsomatic_tonly_step1 {
-    container = "${params.containers.deepsomatic}"
+    container "${params.containers.deepsomatic}"
     label 'process_somaticcaller'
     errorStrategy { task.exitStatus == 1 ? 'ignore' : 'terminate' }
 
@@ -91,7 +91,7 @@ process deepsomatic_tonly_step1 {
 
 //Step 2 can run in CPU or GPU mode for now use only CPUs
 process deepsomatic_step2 {
-    container = "${params.containers.deepsomatic}"
+    container "${params.containers.deepsomatic}"
     label 'process_somaticcaller'
     errorStrategy { task.exitStatus == 1 ? 'ignore' : 'terminate' }
 
@@ -123,7 +123,7 @@ process deepsomatic_step2 {
 }
 
 process deepsomatic_tonly_step2 {
-    container = "${params.containers.deepsomatic}"
+    container "${params.containers.deepsomatic}"
     label 'process_somaticcaller'
     errorStrategy { task.exitStatus == 1 ? 'ignore' : 'terminate' }
 
@@ -157,7 +157,7 @@ process deepsomatic_tonly_step2 {
 
 //Step 3 DV
 process deepsomatic_step3 {
-    container = "${params.containers.deepsomatic}"
+    container "${params.containers.deepsomatic}"
     label 'process_somaticcaller'
     errorStrategy { task.exitStatus == 1 ? 'ignore' : 'terminate' }
 
@@ -188,7 +188,7 @@ process deepsomatic_step3 {
 
 
 process bcfconcat {
-    container = "${params.containers.logan}"
+    container "${params.containers.logan}"
     label 'process_low'
 
     input:

modules/local/deepvariant.nf

@@ -12,7 +12,7 @@ any form of indel realignment,
 
 //Deep Variant
 process deepvariant_step1 {
-    container = "${params.containers.deepvariant}"
+    container "${params.containers.deepvariant}"
     label 'process_somaticcaller'
 
     input:
@@ -46,7 +46,7 @@ process deepvariant_step1 {
 
 //Step 2 requires GPU
 process deepvariant_step2 {
-    container = "${params.containers.deepvariant}"
+    container "${params.containers.deepvariant}"
     //clusterOptions '--gres=lscratch:100,gpu:p100:1  --partition=gpu'
     label 'process_somaticcaller'
 
@@ -79,7 +79,7 @@ process deepvariant_step2 {
 
 //Step 3 DV
 process deepvariant_step3 {
-    container = "${params.containers.deepvariant}"
+    container "${params.containers.deepvariant}"
     label 'process_somaticcaller'
 
     input:
@@ -113,7 +113,7 @@ process deepvariant_step3 {
 
 
 process bcfconcat {
-    container = "${params.containers.logan}"
+    container "${params.containers.logan}"
     label 'process_low'
 
     input:
@@ -138,7 +138,7 @@ process bcfconcat {
 
 
 process glnexus {
-    container = "${params.containers.logan}"
+    container "${params.containers.logan}"
     label 'process_medium'
 
     input: