Author: Steffen Moeller
Last-Update: 2020-08-03 12:22:57 +0200
Description: Reset some timeout values to pass tests, adjust file name for salmon 1.3.0
Forwarded: Yes (https://github.com/BIMSBbioinfo/pigx_rnaseq/pull/79)

Index: pigx-rnaseq/test.sh.in
===================================================================
--- pigx-rnaseq.orig/test.sh.in
+++ pigx-rnaseq/test.sh.in
@@ -30,4 +30,4 @@ if ! test -f "${srcdir}/tests/output/rep
 then
   echo "ERROR: could not find report for STAR"
   exit 1
-fi
\ No newline at end of file
+fi
Index: pigx-rnaseq/etc/settings.yaml.in
===================================================================
--- pigx-rnaseq.orig/etc/settings.yaml.in
+++ pigx-rnaseq/etc/settings.yaml.in
@@ -10,7 +10,7 @@ execution:
   jobs: 6
   nice: 19
   cluster:
-    missing-file-timeout: 120
+    missing-file-timeout: 240
     memory: 8G
     stack: 128M
     queue: all
Index: pigx-rnaseq/tests/settings.yaml
===================================================================
--- pigx-rnaseq.orig/tests/settings.yaml
+++ pigx-rnaseq/tests/settings.yaml
@@ -5,6 +5,13 @@ locations:
   cdna-fasta: sample_data/sample.cdna.fasta
   gtf-file: sample_data/sample.gtf
 
+execution:
+  submit-to-cluster: no
+  jobs: 1
+  cluster:
+    missing-file-timeout: 120
+
+
 organism: ''
 
 DEanalyses:
Index: pigx-rnaseq/tests/test_salmon/test_salmon_index.sh.in
===================================================================
--- pigx-rnaseq.orig/tests/test_salmon/test_salmon_index.sh.in
+++ pigx-rnaseq/tests/test_salmon/test_salmon_index.sh.in
@@ -26,7 +26,7 @@ head -n 2 ${samplesheet} > ${tmp_samples
 ${builddir}/pigx-rnaseq -s ${tmp_settings} --target salmon_index ${tmp_samplesheet}
 
 rm ${tmp_settings} ${tmp_samplesheet}
-if ! test -f ${testfolder}/salmon_index/sa.bin
+if ! test -f ${testfolder}/salmon_index/pos.bin
 then
   echo "ERROR: failed the SALMON indexing test"
   exit 1
Index: pigx-rnaseq/pigx_rnaseq.py
===================================================================
--- pigx-rnaseq.orig/pigx_rnaseq.py
+++ pigx-rnaseq/pigx_rnaseq.py
@@ -113,7 +113,7 @@ targets = {
         'description': "Produce a comprehensive report.  This is the default target.",
         'files':
       [os.path.join(OUTPUT_DIR, 'star_index', "SAindex"),
-            os.path.join(OUTPUT_DIR, 'salmon_index', "sa.bin"),
+            os.path.join(OUTPUT_DIR, 'salmon_index', "pos.bin"),
             os.path.join(MULTIQC_DIR, 'multiqc_report.html')] +
 	  [os.path.join(COUNTS_DIR, "raw_counts", "counts_from_SALMON.transcripts.tsv"),
             os.path.join(COUNTS_DIR, "raw_counts", "counts_from_SALMON.genes.tsv"),
@@ -167,7 +167,7 @@ targets = {
     'salmon_index' : {
         'description': "Create SALMON index file.",
         'files':
-          [os.path.join(OUTPUT_DIR, 'salmon_index', "sa.bin")]
+          [os.path.join(OUTPUT_DIR, 'salmon_index', "pos.bin")]
     },
     'salmon_quant' : {
         'description': "Calculate read counts per transcript using SALMON.",
@@ -321,7 +321,7 @@ rule salmon_index:
   input:
       CDNA_FASTA
   output:
-      salmon_index_file = os.path.join(OUTPUT_DIR, 'salmon_index', "sa.bin")
+      salmon_index_file = os.path.join(OUTPUT_DIR, 'salmon_index', "pos.bin")
   params:
       salmon_index_dir = os.path.join(OUTPUT_DIR, 'salmon_index')
   log: os.path.join(LOG_DIR, 'salmon_index.log')