subread nf: add nf config and test files

src/nf_modules/htseq/tests.sh

@@ -8,7 +8,7 @@
 if [ -x "$(command -v singularity)" ]; then
 ./nextflow src/nf_modules/htseq/htseq.nf \
   -c src/nf_modules/htseq/htseq.config \
-  -profile docker \
+  -profile singularity \
   --gtf "data/tiny_dataset/annot/tiny.gff" \
   --bam "data/tiny_dataset/map/tiny_v2.bam" \
   -resume

src/nf_modules/subread/subread.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: sort_bam {
+        container = "samtools:1.7"
+        cpus = 1
+      }
+      withName: counting {
+        container = "subread:1.6.4"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: sort_bam {
+        container = "file://bin/samtools:1.7.img"
+        cpus = 1
+      }
+      withName: counting {
+        container = "file://bin/subread:1.6.4.img"
+        cpus = 1
+      }
+    }
+  }
+  psmn{
+    process{
+      withName: sort_bam {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+      }
+      withName: counting {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "subread/1.6.4"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+      }
+    }
+  }
+  ccin2p3_conda {
+    process{
+      withName: sort_bam {
+        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
+        conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+        "
+        cpus = 1
+        queue = 'huge'
+      }
+      withName: counting {
+        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
+        conda = "/sps/lbmc/common/miniconda3/envs/subread_1.6.4"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+        "
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: sort_bam {
+        container = "/sps/lbmc/common/singularity/samtools:1.7.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+        "
+        cpus = 1
+        queue = 'huge'
+      }
+      withName: counting {
+        container = "/sps/lbmc/common/singularity/subread:1.6.4.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+        "
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
+}

src/nf_modules/subread/subread.nf

+params.bam = "$baseDir/data/bam/*.bam"
+params.gtf = "$baseDir/data/annotation/*.gtf"
+
+log.info "bam files : ${params.bam}"
+log.info "gtf files : ${params.gtf}"
+
+Channel
+  .fromPath( params.bam )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set { bam_files }
+Channel
+  .fromPath( params.gtf )
+  .ifEmpty { error "Cannot find any gtf file matching: ${params.gtf}" }
+  .set { gtf_file }
+
+process sort_bam {
+  tag "$file_id"
+  cpus 4
+
+  input:
+    set file_id, file(bam) from bam_files
+
+  output:
+    set file_id, "*_sorted.sam" into sorted_bam_files
+
+  script:
+"""
+# sort bam by name
+samtools sort -@ ${task.cpus} -n -O SAM -o ${file_id}_sorted.sam ${bam}
+"""
+}
+
+process counting {
+  tag "$file_id"
+  publishDir "results/quantification/", mode: 'copy'
+
+  input:
+  set file_id, file(bam) from sorted_bam_files
+  file gtf from gtf_file
+
+  output:
+  file "*.count" into count_files
+
+  script:
+"""
+featureCounts ${bam} -a ${gtf} -p \
+  -o ${file_id}.count \
+  -R BAM
+"""
+}
+

src/nf_modules/subread/tests.sh

+./nextflow src/nf_modules/subread/subread.nf \
+  -c src/nf_modules/subread/subread.config \
+  -profile docker \
+  --gtf "data/tiny_dataset/annot/tiny.gff" \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/subread/subread.nf \
+  -c src/nf_modules/subread/subread.config \
+  -profile singularity \
+  --gtf "data/tiny_dataset/annot/tiny.gff" \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
+fi