Merge branch 'fusions' into 'dev'

Fusions

See merge request epi2melabs/workflow-containers/wf-transcriptomes!64

README.md

@@ -138,7 +138,7 @@ do:
 ```shell
 mkdir jaffal_data_dir
 cd jaffal_data_dir/
-wf-transcriptomes/download_jaffal_references.sh
+wf-transcriptomes/subworkflows/JAFFAL/load_jaffal_references.sh
 ````
 
 To use alternative genome and annotation files, they should be prepared as described
@@ -147,7 +147,7 @@ To use alternative genome and annotation files, they should be prepared as descr
 **Specifying the location of the JAFFA code and reference directories**
 
 `--jaffal_dir`
-This is the directory made by running install_jaffa.sh as shown above
+Full path to the directory made by running install_jaffa.sh as shown above. eg: /home/wf-trnascriptomes/JAFFA
 
 `--jaffal_refBase`
 The directory containing the reference data prepared for use with JAFFAL

bin/report.py

@@ -798,20 +798,16 @@ def seq_stats_tabs(report, sample_ids, stats):
     section.plot(Tabs(tabs=tabs))
 
 
-def jaffal_table(report, sample_ids, result_csvs):
+def jaffal_table(report, result_csv):
     """Make a table of fusion transcripts identified by JAFFAL."""
     cols = [
         'sample_id', 'fusion genes', 'chrom1', 'chrom2', 'spanning reads',
         'classification', 'known']
-    dfs = []
-    for csv, sid in zip(result_csvs, sample_ids):
-        df = pd.read_csv(csv)
-        df['sample_id'] = sid
+
+    df = pd.read_csv(result_csv)
     sid_col = df.pop('sample_id')
     df.insert(0, 'sample_id', sid_col)
-        dfs.append(df)
 
-    df = pd.concat(dfs)
     df = df[cols]
     df['chroms'] = df.chrom1.astype(str) + ':' + df.chrom2.astype(str)
     df.rename(columns={
@@ -874,7 +870,7 @@ def main():
         "--cluster_qc_dirs", required=False, type=str, default=None, nargs='*',
         help="Directory with various cluster quality csvs")
     parser.add_argument(
-        "--jaffal_csv", required=False, type=str, default=None,  nargs='*',
+        "--jaffal_csv", required=False, type=str, default=None,
         help="Path to JAFFAL results csv")
     parser.add_argument('--denovo', dest='denovo', action='store_true')
 
@@ -921,8 +917,8 @@ def main():
     if args.cluster_qc_dirs is not None:
         cluster_quality(args.cluster_qc_dirs, report, sample_ids)
 
-    if args.jaffal_csv is not None:
-        jaffal_table(report, sample_ids, args.jaffal_csv)
+    if args.jaffal_csv:
+        jaffal_table(report, args.jaffal_csv)
 
     # Arguments and software versions
     report.add_section(

docs/quickstart.md

@@ -90,7 +90,7 @@ do:
 ```shell
 mkdir jaffal_data_dir
 cd jaffal_data_dir/
-wf-transcriptomes/download_jaffal_references.sh
+wf-transcriptomes/subworkflows/JAFFAL/load_jaffal_references.sh
 ````
 
 To use alternative genome and annotation files, they should be prepared as described
@@ -99,7 +99,7 @@ To use alternative genome and annotation files, they should be prepared as descr
 **Specifying the location of the JAFFA code and reference directories**
 
 `--jaffal_dir`
-This is the directory made by running install_jaffa.sh as shown above
+Full path to the directory made by running install_jaffa.sh as shown above. eg: /home/wf-trnascriptomes/JAFFA
 
 `--jaffal_refBase`
 The directory containing the reference data prepared for use with JAFFAL

main.nf

@@ -282,12 +282,12 @@ process makeReport {
         path "params.json"
         val denovo
         path pychopper_report
+        path jaffal_csv
         tuple val(sample_ids),
               path(seq_summaries),
               path(aln_stats),
               path(gffcmp_dir),
-              path(gff_annotation),
-              path(jaffal_csv)
+              path(gff_annotation)
     output:
         path("wf-transcriptomes-*.html"), emit: report
     script:
@@ -297,6 +297,8 @@ process makeReport {
         def OPT_ALN = denovo ?  '' : "--alignment_stats ${aln_stats}"
         def OPT_DENOVO = denovo ? "--denovo" : ''
         def OPT_PC_REPORT = pychopper_report.name.startsWith('OPTIONAL_FILE') ? '' : "--pychop_report ${pychopper_report}"
+        def OPT_JAFFAL_CSV = jaffal_csv.name.startsWith('OPTIONAL_FILE') ? '' : "--jaffal_csv ${jaffal_csv}"
+
     """
     report.py --report $report_name \
     --versions $versions \
@@ -308,7 +310,7 @@ process makeReport {
     --gffcompare_dir $gffcmp_dir \
     --gff_annotation $gff_annotation \
     --transcript_table_cov_thresh $params.transcript_table_cov_thresh \
-    --jaffal_csv $jaffal_csv
+    $OPT_JAFFAL_CSV \
     $OPT_DENOVO
     """
 }
@@ -408,6 +410,9 @@ workflow pipeline {
 
         if (jaffal_refBase){
             gene_fusions(full_len_reads, jaffal_refBase, jaffal_genome, jaffal_annotation)
+            jaffal_out = gene_fusions.out.results_csv.collectFile(keepHeader: true, name: 'jaffal.csv')
+        }else{
+            jaffal_out = file("$projectDir/data/OPTIONAL_FILE_1")
         }
 
         makeReport(
@@ -415,11 +420,11 @@ workflow pipeline {
             workflow_params,
             params.denovo,
             pychopper_report,
+            jaffal_out,
             summariseConcatReads.out.summary
             .join(m.stats)
             .join(run_gffcompare.out.gffcmp_dir)
             .join(merge_gff_bundles.out.gff)
-            .join(gene_fusions.out.results_csv)
             .toList().transpose().toList())
 
         report = makeReport.out.report

subworkflows/JAFFAL/download_jaffal_references.sh

@@ -0,0 +1,5 @@
+#!/bin/sh
+
+#Download the data. We should we move the data out of Figshare?
+wget -O JAFFA_REFERENCE_FILES_HG38_GENCODE22.V2.tar.gz https://figshare.com/ndownloader/files/25410494
+tar -zxvf JAFFA_REFERENCE_FILES_HG38_GENCODE22.V2.tar.gz

subworkflows/JAFFAL/gene_fusions.nf

@@ -22,6 +22,12 @@ process jaffal{
         $params.jaffal_dir/JAFFAL.groovy \
         $fastq
     mv "\$JAFFAOUT/jaffa_results.csv" "\$JAFFAOUT/${sample_id}_jaffa_results.csv"
+
+    # Add sample id column
+    sed "s/\$/,${sample_id}/" \$JAFFAOUT/${sample_id}_jaffa_results.csv > tmp1
+    # Add header
+    sed "1 s/${sample_id}/sample_id/" tmp1 > tmp2
+    mv tmp2 \$JAFFAOUT/${sample_id}_jaffa_results.csv
     """
 }