Fix: Vars and output dirs in demultiplexing_illumina workkflow

segrelab · May 15, 2021 · fa10fb1 · fa10fb1
1 parent f0f41df
commit fa10fb1
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Showing 6 changed files with 65 additions and 8 deletions.
diff --git a/micone/pipelines/configs/denoise_cluster.conf b/micone/pipelines/configs/denoise_cluster.conf
@@ -0,0 +1,31 @@
+// -*- mode: groovy -*-
+
+/*
+* Reference for useful snippets:
+    publishDir "${params.output_dir}/${f1}/${f2}/${f3}/${meta.id}",
+        saveAs: { filename -> filename.split("/")[1] },
+        mode: 'copy',
+        overwrite: true
+    f1, f2, f3 = getHierarchy("${task.process}")
+*/
+
+params {
+    denoise_cluster {
+        sequence_processing {
+            // Demultiplexing illumina workflow
+            'demultiplexing_illumina' {
+                rev_comp_barcodes = "False"
+                rev_comp_mapping_barcodes = "False"
+            }
+            'join_reads' {
+                min_overlap = 6
+                perc_max_diff = 8
+            }
+            // Trim filter fixed workflow
+            'export_visualization' {
+                seq_samplesize = 10000
+            }
+            // TODO: Demultiplexing 454 workflow
+        }
+    }
+}
diff --git a/micone/pipelines/configs/process.conf b/micone/pipelines/configs/process.conf
@@ -0,0 +1,6 @@
+// -*- mode: groovy -*-
+
+// trace
+// dag
+// conda envs
+// env
diff --git a/micone/pipelines/functions/functions.nf b/micone/pipelines/functions/functions.nf
@@ -0,0 +1,12 @@
+def get_samplesheet_paths(LinkedHashMap row) {
+    def meta = [:]
+    meta.id           = row.sample
+    meta.single_end   = row.single_end.toBoolean()
+    meta.strandedness = row.strandedness
+    return meta
+}
+
+def getHierarchy(String task_process) {
+    def hierarchy = task_process.split(":")
+    return hierarchy.collect { it.replaceAll("_workflow", "") }
+}
diff --git a/micone/pipelines/modules/denoise_cluster/sequence_processing/demultiplexing_illumina.nf b/micone/pipelines/modules/denoise_cluster/sequence_processing/demultiplexing_illumina.nf
@@ -8,9 +8,9 @@ process demultiplexing_illumina {
         tuple val(meta), file('*_demux.qza')
     script:
         meta.demultiplexing = "illumina"
-        def rev_comp_barcodes = params.denoise_cluster.sequence_processing['demultiplexing_illumina']['rev_comp_barcodes']
-        def rev_comp_mapping_barcodes = params.denoise_cluster.sequence_processing['demultiplexing_illumina']['rev_comp_mapping_barcodes']
-        def rcb = rev_comp_barcodes == 'True' ? '--p-rev-comp-barcodes' : '--p-no-rev-comp-barcodes'
-        def rcmb = rev_comp_mapping_barcodes == 'True' ? '--p-rev-comp-mapping-barcodes' : '--p-no-rev-comp-mapping-barcodes'
+        rev_comp_barcodes = params.denoise_cluster.sequence_processing['demultiplexing_illumina']['rev_comp_barcodes']
+        rev_comp_mapping_barcodes = params.denoise_cluster.sequence_processing['demultiplexing_illumina']['rev_comp_mapping_barcodes']
+        rcb = rev_comp_barcodes == 'True' ? '--p-rev-comp-barcodes' : '--p-no-rev-comp-barcodes'
+        rcmb = rev_comp_mapping_barcodes == 'True' ? '--p-rev-comp-mapping-barcodes' : '--p-no-rev-comp-mapping-barcodes'
         template 'denoise_cluster/sequence_processing/demultiplex_illumina.sh'
 }
diff --git a/micone/pipelines/modules/denoise_cluster/sequence_processing/export_sequences.nf b/micone/pipelines/modules/denoise_cluster/sequence_processing/export_sequences.nf
@@ -2,11 +2,15 @@
 process export_sequences {
     label 'qiime2'
     tag "${meta.id}"
-    publishDir "${params.output_dir}/${task.process}/${meta.id}", saveAs: { filename -> filename.split("/")[1] }, mode: 'copy', overwrite: true
+    publishDir "${params.output_dir}/${f1}/${f2}/${f3}/${meta.id}",
+        saveAs: { filename -> filename.split("/")[1] },
+        mode: 'copy',
+        overwrite: true
     input:
         tuple val(meta), file(demux_artifact)
     output:
         tuple val(meta), file('demux_seqs/*.fastq.gz'), file('demux_seqs/MANIFEST')
     script:
+        f1, f2, f3 = getHierarchy("${task.process}")
         template 'denoise_cluster/sequence_processing/export_sequences.py'
 }
diff --git a/micone/pipelines/modules/denoise_cluster/sequence_processing/join_reads.nf b/micone/pipelines/modules/denoise_cluster/sequence_processing/join_reads.nf
@@ -2,13 +2,17 @@
 process join_reads {
     label 'qiime1'
     tag "${meta.id}"
-    publishDir "${params.output_dir}/${task.process}/${meta.id}", saveAs: { filename -> filename.split("/")[1] }, mode: 'copy', overwrite: true
+    publishDir "${params.output_dir}/${f1}/${f2}/${f3}/${meta.id}",
+        saveAs: { filename -> filename.split("/")[1] },
+        mode: 'copy',
+        overwrite: true
     input:
         tuple val(meta), val(sequence_files), file(barcode_file)
     output:
         tuple val(meta), file('joined_reads/*_reads.fastq.gz'), file('joined_reads/*_barcodes.fastq.gz')
     script:
-        def min_overlap = params.denoise_cluster.sequence_processing['join_reads']['min_overlap']
-        def perc_max_diff = params.denoise_cluster.sequence_processing['join_reads']['perc_max_diff']
+        f1, f2, f3 = getHierarchy("${task.process}")
+        min_overlap = params.denoise_cluster.sequence_processing['join_reads']['min_overlap']
+        perc_max_diff = params.denoise_cluster.sequence_processing['join_reads']['perc_max_diff']
         template 'denoise_cluster/sequence_processing/join_reads.sh'
 }