Adopt BCCDC-PHL/FluViewer

bin/tools.py

@@ -12,7 +12,7 @@ def flex_translate(nt_seq, debug=False):
 		- An integer indicating the best reading frame that was used for translation (0, 1, or 2)
 		- An integer indicating the number of stop codons in this best translation candidate
 	"""
-	min_count = np.Inf
+	min_count = np.inf
 	best_seq = None
 	best_frame = -1
 

modules/clade_calling.nf

@@ -14,7 +14,7 @@ process clade_calling {
 
     output:
     tuple val(sample_id), path("*nextclade*"), emit: nextclade, optional: true
-    tuple val(sample_id), path("${sample_id}_clade_calling__provenance.yml"), emit: provenance, optional: true
+    tuple val(sample_id), path("${sample_id}_clade_calling_provenance.yml"), emit: provenance, optional: true
 
     script:
     """

modules/fluviewer.nf

@@ -6,40 +6,42 @@ process fluviewer {
     errorStrategy { (task.exitStatus == 2 && task.attempt <= maxRetries) ? 'retry' : 'ignore' } 
     maxRetries 5
 
-    publishDir "${params.outdir}/${params.run_name}/${params.pipeline_short_name}-v${params.pipeline_minor_version}/${sample_id}", pattern: "${sample_id}_fluviewer/${sample_id}*", mode:'copy', saveAs: { filename -> filename.split("/").last() }
-    publishDir "${params.outdir}/${params.run_name}/${params.pipeline_short_name}-v${params.pipeline_minor_version}/${sample_id}", pattern: "${sample_id}_fluviewer/*tsv", mode:'copy', saveAs: { filename -> filename.split("/").last() }
-    publishDir "${params.outdir}/${params.run_name}/${params.pipeline_short_name}-v${params.pipeline_minor_version}/${sample_id}", pattern: "${sample_id}_fluviewer/spades_output", mode:'copy', saveAs: { filename -> "spades_output" }
+    publishDir "${params.outdir}/${params.run_name}/${params.pipeline_short_name}-v${params.pipeline_minor_version}/${sample_id}", pattern: "${sample_id}*", mode:'copy', saveAs: { filename -> filename.split("/").last() }
+    publishDir "${params.outdir}/${params.run_name}/${params.pipeline_short_name}-v${params.pipeline_minor_version}/${sample_id}", pattern: "*tsv", mode:'copy', saveAs: { filename -> filename.split("/").last() }
+    //publishDir "${params.outdir}/${params.run_name}/${params.pipeline_short_name}-v${params.pipeline_minor_version}/${sample_id}", pattern: "${sample_id}_fluviewer/spades_output", mode:'copy', saveAs: { filename -> "spades_output" }
     publishDir "${params.outdir}/${params.run_name}/${params.pipeline_short_name}-v${params.pipeline_minor_version}/${sample_id}", pattern: ".*", mode:'copy'
-    publishDir "${params.outdir}/${params.run_name}/${params.pipeline_short_name}-v${params.pipeline_minor_version}/${sample_id}", pattern: "${sample_id}_fluviewer/logs", mode:'copy', saveAs: { filename -> "fluviewer_logs" }
+    publishDir "${params.outdir}/${params.run_name}/${params.pipeline_short_name}-v${params.pipeline_minor_version}/${sample_id}", pattern: "logs", mode:'copy', saveAs: { filename -> "fluviewer_logs" }
     publishDir "${params.outdir}/${params.run_name}/${params.pipeline_short_name}-v${params.pipeline_minor_version}/${sample_id}", pattern: ".exitcode", mode:'copy'
     publishDir "${params.outdir}/${params.run_name}/${params.pipeline_short_name}-v${params.pipeline_minor_version}/${sample_id}", pattern: ".command.*", mode:'copy'
 
     input:
     tuple val(sample_id), path(reads_1), path(reads_2), path(db)
 
     output:
-    tuple val(sample_id), path("${sample_id}_fluviewer/${sample_id}*.bam"), emit: alignment
-    tuple val(sample_id), path("${sample_id}_fluviewer/${sample_id}*.bam.bai"), emit: alignmentindex, optional: true
-    tuple val(sample_id), path("${sample_id}_fluviewer/${sample_id}*report.tsv"), emit: reports, optional: true
-    tuple val(sample_id), path("${sample_id}_fluviewer/${sample_id}*_consensus.fa"), emit: consensus_seqs, optional: true
-    tuple val(sample_id), path("${sample_id}_fluviewer/${sample_id}*consensus_seqs.fa"), emit: consensus_main
-    tuple val(sample_id), path("${sample_id}_fluviewer/${sample_id}*_HPAI.tsv"), emit: HPAI, optional: true
-    tuple val(sample_id), path("${sample_id}_fluviewer/${sample_id}*_cov.png"), emit: coverage_plot, optional: true
-    tuple val(sample_id), path("${sample_id}_fluviewer/${sample_id}*_variants.vcf"), emit: vcf, optional: true
-    tuple val(sample_id), path("${sample_id}_fluviewer/logs"), emit: fluviewer_logs
-    tuple val(sample_id), path("${sample_id}_FluViewer_provenance.yml"), emit: provenance
-    tuple val(sample_id), path("${sample_id}_fluviewer/${sample_id}*_mapping_refs.fa"), emit: ref_seqs_for_mapping, optional: true
-    tuple val(sample_id), path("${sample_id}_fluviewer/contigs_blast.tsv"), emit: contig_blast_results, optional: true
-    tuple val(sample_id), path("${sample_id}_fluviewer/spades_output"), emit: spades_results, optional: true
-    tuple val(sample_id), path("${sample_id}_fluviewer/${sample_id}*.png"), emit: depth_cov_plot, optional: true
+    tuple val(sample_id), path("${sample_id}*.bam"), emit: alignment
+    tuple val(sample_id), path("${sample_id}*.bam.bai"), emit: alignmentindex, optional: true
+    tuple val(sample_id), path("${sample_id}*report.tsv"), emit: reports, optional: true
+    tuple val(sample_id), path("${sample_id}*_consensus.fa"), emit: consensus_seqs, optional: true
+    tuple val(sample_id), path("${sample_id}*consensus_seqs.fa"), emit: consensus_main
+    tuple val(sample_id), path("${sample_id}*_HPAI.tsv"), emit: HPAI, optional: true
+    tuple val(sample_id), path("${sample_id}*_cov.png"), emit: coverage_plot, optional: true
+    tuple val(sample_id), path("${sample_id}*_variants.vcf"), emit: vcf, optional: true
+    tuple val(sample_id), path("logs"), emit: fluviewer_logs
+    tuple val(sample_id), path("${sample_id}_fluviewer_provenance.yml"), emit: provenance
+    tuple val(sample_id), path("${sample_id}*_mapping_refs.fa"), emit: ref_seqs_for_mapping, optional: true
+    tuple val(sample_id), path("${sample_id}_contigs_blast.tsv"), emit: contig_blast_results, optional: true
+    //tuple val(sample_id), path("${sample_id}_fluviewer/spades_output"), emit: spades_results, optional: true
+    tuple val(sample_id), path("${sample_id}*.png"), emit: depth_cov_plot, optional: true
 
     script:
     garbage_collection = params.keep_interfiles ? '-g' : ''
+    OUTPATH="${params.outdir}/${params.run_name}/${params.pipeline_short_name}-v${params.pipeline_minor_version}/${sample_id}"
+
     """
     printf -- "- process_name: fluviewer\\n"                  >> ${sample_id}_fluviewer_provenance.yml
     printf -- "  tools:\\n"                                   >> ${sample_id}_fluviewer_provenance.yml
-    printf -- "    - tool_name: FluViewer\\n"                 >> ${sample_id}_fluviewer_provenance.yml
-    printf -- "      tool_version: \$(FluViewer | sed -n '4 p')\\n" >> ${sample_id}_FluViewer_provenance.yml
+    printf -- "    - tool_name: fluviewer\\n"                 >> ${sample_id}_fluviewer_provenance.yml
+    printf -- "      tool_version: \$(fluviewer --version)\\n" >> ${sample_id}_fluviewer_provenance.yml
     printf -- "  databases:\\n"                               >> ${sample_id}_fluviewer_provenance.yml
     printf -- "    - database_name: ${db}\\n"                 >> ${sample_id}_fluviewer_provenance.yml
     printf -- "      database_path: \$(readlink -f ${db})\\n" >> ${sample_id}_fluviewer_provenance.yml
@@ -60,36 +62,52 @@ process fluviewer {
 	--max-memory 40 && EXITCODE=\$?) \
 	|| EXITCODE=\$?
 
+    function SAFE_EXIT {
+        EXITCODE=\$1
+        OUTPATH=\$2
+
+        echo \$EXITCODE > .exitcode
+        cp .command.* \$OUTPATH
+        cp .exitcode \$OUTPATH
+        exit \$EXITCODE
+    }
+
+    OUTPATH=${params.outdir}/${params.run_name}/${params.pipeline_short_name}-v${params.pipeline_minor_version}/${sample_id}
+
+    if [[ \$OUTPATH != /* ]]; then              # catch case where params.outdir is relative path and fix OUTPATH variable
+        OUTPATH=${workflow.launchDir}/\$OUTPATH
+    fi
+
+
+    if [ \$EXITCODE -ne 0 ]; then 
+        echo "fluviewer exited with non-zero exit code. Skipping remaining analyses."
+        SAFE_EXIT \$EXITCODE \$OUTPATH
+    fi
+
     echo "Extracting NA and HA consensus sequences..."
 
-    if [ `grep "|HA|" ${sample_id}_fluviewer/${sample_id}*consensus_seqs.fa` ]; then 
-        grep -A1 "|HA|" ${sample_id}_fluviewer/${sample_id}*consensus_seqs.fa > ${sample_id}_fluviewer/${sample_id}_HA_consensus.fa
+
+    if [ `grep "|HA|" ${sample_id}*consensus_seqs.fa` ]; then 
+        grep -A1 "|HA|" ${sample_id}*consensus_seqs.fa > ${sample_id}_HA_consensus.fa
     else
         echo "No HA consensus sequence generated."
     fi
 
-    if [ `grep "|NA|" ${sample_id}_fluviewer/${sample_id}*consensus_seqs.fa` ]; then 
-        grep -A1 "|NA|" ${sample_id}_fluviewer/${sample_id}*consensus_seqs.fa > ${sample_id}_fluviewer/${sample_id}_NA_consensus.fa
+    if [ `grep "|NA|" ${sample_id}*consensus_seqs.fa` ]; then 
+        grep -A1 "|NA|" ${sample_id}*consensus_seqs.fa > ${sample_id}_NA_consensus.fa
     else
         echo "No NA consensus sequence generated."
     fi
 
-    if [[ ! -f ${sample_id}_fluviewer/${sample_id}_HA_consensus.fa ]]; then
+    if [[ ! -f ${sample_id}_HA_consensus.fa ]]; then
         echo "HA segment consensus not generated. Skipping FindCleave.py..."
     else
-	python ${projectDir}/bin/FindCleave.py -i ${sample_id}_fluviewer/${sample_id}_HA_consensus.fa -o ${sample_id}_fluviewer/${sample_id}_HPAI.tsv
+	python ${projectDir}/bin/FindCleave.py -i ${sample_id}_HA_consensus.fa -o ${sample_id}_HPAI.tsv
         echo "Finished running FindCleave.py."
     fi
 
-  echo \$EXITCODE > .exitcode
-
-  OUTPATH=${params.outdir}/${params.run_name}/${params.pipeline_short_name}-v${params.pipeline_minor_version}/${sample_id}
-  if [[ \$OUTPATH != /* ]]; then 
-    OUTPATH=${workflow.launchDir}/\$OUTPATH
-  fi
+    ln -s analysis_by_stage/02_blast_contigs/${sample_id}_contigs_blast.tsv ${sample_id}_contigs_blast.tsv 
 
-  cp .command.* \$OUTPATH
-  cp .exitcode \$OUTPATH
-  exit \$EXITCODE
-  """
+    SAFE_EXIT \$EXITCODE \$OUTPATH
+    """
 }