updates

.github/scripts/check_outputs.py

@@ -38,6 +38,12 @@ def check_expected_files_exist(output_dir, sample_ids):
     """
     for sample_id in sample_ids:
         expected_files = [
+            f"fastq/fluviewer-nf-v0.2/{sample_id}/{sample_id}_fluviewer_alignment.bam",
+            f"fastq/fluviewer-nf-v0.2/{sample_id}/{sample_id}_fluviewer_alignment.bam.bai",
+            f"fastq/fluviewer-nf-v0.2/{sample_id}/{sample_id}_fluviewer_depth_of_cov.png",
+            f"fastq/fluviewer-nf-v0.2/{sample_id}/{sample_id}_fluviewer_mapping_refs.fa",
+            f"fastq/fluviewer-nf-v0.2/{sample_id}/{sample_id}_fluviewer_report.tsv",
+            f"fastq/fluviewer-nf-v0.2/{sample_id}/{sample_id}_genoflu.tsv",
         ]
 
         for expected_file in expected_files:

environments/fluviewer.yml

@@ -209,4 +209,4 @@ dependencies:
   - zlib=1.2.13=hd590300_5
   - zstd=1.5.5=hfc55251_0
   - pip:
-      - fluviewer
+      - FluViewer==0.1.11

main.nf

@@ -106,7 +106,7 @@ workflow {
     ch_provenance = ch_provenance.join(hash_files.out.provenance).map{ it ->    [it[0], it[1] << it[2]] }
     ch_provenance = ch_provenance.join(fastp.out.provenance).map{ it ->         [it[0], it[1] << it[2]] }
     ch_provenance = ch_provenance.join(cutadapt.out.provenance).map{ it ->      [it[0], it[1] << it[2]] }
-    // ch_provenance = ch_provenance.join(FluViewer.out.provenance).map{ it ->     [it[0], it[1] << it[2]] }    
+    ch_provenance = ch_provenance.join(fluviewer.out.provenance).map{ it ->     [it[0], it[1] << it[2]] }    
     // ch_provenance = ch_provenance.join(CLADE_CALLING.out.provenance).map{ it -> [it[0], it[1] << it[2]] }
     // ch_provenance = ch_provenance.join(GENOFLU.out.provenance).map{ it ->       [it[0], it[1] << it[2]] }
     collect_provenance(ch_provenance)

modules/hash_files.nf

@@ -13,7 +13,9 @@ process hash_files {
     """
     shasum -a 256 ${files_to_hash} | tr -s ' ' ',' > ${sample_id}_${file_type}.sha256.csv
     while IFS=',' read -r hash filename; do
-      printf -- "- input_filename: \$filename\\n  input_path: \$(realpath \$filename)\\n  sha256: \$hash\\n" >> ${sample_id}_${file_type}_provenance.yml
+      printf -- "- input_filename: \$filename\\n"  >> ${sample_id}_${file_type}_provenance.yml;
+      printf -- "  file_type: ${file_type}\\n"     >> ${sample_id}_${file_type}_provenance.yml;
+      printf -- "  sha256: \$hash\\n"              >> ${sample_id}_${file_type}_provenance.yml;
     done < ${sample_id}_${file_type}.sha256.csv
     """
 }