Add: sample_filter param to demultiplexing module

segrelab · Mar 1, 2023 · 479c7b5 · 479c7b5
1 parent 1bd0167
commit 479c7b5
Show file tree

Hide file tree

Showing 3 changed files with 12 additions and 0 deletions.
diff --git a/micone/pipelines/configs/sequence_processing.config b/micone/pipelines/configs/sequence_processing.config
@@ -15,6 +15,9 @@ params {
                 rev_comp_barcodes = false
                 rev_comp_mapping_barcodes = false
             }
+            'export_sequences' {
+                sample_filter = ""
+            }
         }
         // Trim filter workflow
         trimming {

diff --git a/micone/pipelines/modules/sequence_processing/demultiplexing/export_sequences.nf b/micone/pipelines/modules/sequence_processing/demultiplexing/export_sequences.nf
@@ -15,5 +15,6 @@ process export_sequences {
     script:
         String task_process = "${task.process}"
         f = getHierarchy(task_process)
+        sample_filter = params.sequence_processing.demultiplexing['export_sequences']['sample_filter']
         template 'sequence_processing/demultiplexing/export_sequences.sh'
 }
diff --git a/micone/pipelines/templates/sequence_processing/demultiplexing/export_sequences.sh b/micone/pipelines/templates/sequence_processing/demultiplexing/export_sequences.sh
@@ -3,3 +3,11 @@
 qiime tools export \
     --input-path "${demux_artifact}" \
     --output-path demux_seqs
+
+if [[ '${sample_filter}' ]]; then
+    cd demux_seqs || exit
+    ls -1 | grep -v '${sample_filter}' | xargs rm -f
+    mv MANIFEST MANIFEST_OLD
+    sed '/sample-id\|${sample_filter}/!d' MANIFEST_OLD >MANIFEST
+    rm MANIFEST_OLD
+fi