BuildIndices tweaks from a test run

common-workflow-lab · Apr 17, 2024 · 1ae25d8 · 1ae25d8
1 parent 5525624
commit 1ae25d8
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Showing 3 changed files with 19 additions and 17 deletions.
diff --git a/wdl2cwl/tests/cwl_files/BuildIndices.cwl b/wdl2cwl/tests/cwl_files/BuildIndices.cwl
@@ -127,7 +127,7 @@ steps:
               - entryname: script.bash
                 entry: |4
 
-                    set -eo pipefail
+                    set -exo pipefail
 
                     ## download fasta
                     wget $("ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_" + inputs.organism + "/release_" + inputs.gtf_version)/$("GRC" + inputs.organism_prefix + "38.primary_assembly.genome.fa").gz
@@ -230,7 +230,7 @@ steps:
               - entryname: script.bash
                 entry: |4+
 
-                    set -eo pipefail
+                    set -exo pipefail
 
 
                     # index the fasta file
@@ -305,7 +305,7 @@ steps:
               - entryname: script.bash
                 entry: |4
 
-                    set -eo pipefail
+                    set -exo pipefail
 
                     mkdir star
                     STAR --runMode genomeGenerate \
@@ -394,9 +394,9 @@ steps:
               - entryname: script.bash
                 entry: |4
 
-                    set -eo pipefail
+                    set -exo pipefail
 
-                    /script/modify_gtf_$(inputs.organism).sh $(inputs.references.genome_fa.path) $(inputs.references.annotation_gtf.path)
+                    bash -ex /script/modify_gtf_$(inputs.organism).sh $(inputs.references.genome_fa.path) $(inputs.references.annotation_gtf.path)
 
                     mkdir star
                     STAR --runMode genomeGenerate \
@@ -629,24 +629,25 @@ steps:
                 entry: |4+
 
 
+                    set -ex
                     HISAT2_DIR=/opt/tools/hisat2-2.1.0
 
                     # Compressed fasta required here
-                    gzip $(inputs.references.genome_fa.path)
+                    gzip $(inputs.references.genome_fa.path) -c > $(inputs.references.genome_fa.basename).gz
 
                     # download snp file
                     wget http://hgdownload.cse.ucsc.edu/goldenPath/$(inputs.genome_short_string)/database/$("snp" + inputs.dbsnp_version + "Common.txt").gz
                     gunzip $("snp" + inputs.dbsnp_version + "Common.txt").gz
 
                     # extract snps, splice sites, and exon information
-                    $HISAT2_DIR/hisat2_extract_snps_UCSC.py $(inputs.references.genome_fa.path).gz $("snp" + inputs.dbsnp_version + "Common.txt") genome
+                    $HISAT2_DIR/hisat2_extract_snps_haplotypes_UCSC.py $(inputs.references.genome_fa.basename).gz $("snp" + inputs.dbsnp_version + "Common.txt") genome
                     $HISAT2_DIR/hisat2_extract_splice_sites.py $(inputs.references.annotation_gtf.path) > genome.ss
                     $HISAT2_DIR/hisat2_extract_exons.py $(inputs.references.annotation_gtf.path) > genome.exon
 
                     # build the hisat2 reference
                     $HISAT2_DIR/hisat2-build \
                       -p 8 \
-                      genome.fa \
+                      $(inputs.references.genome_fa.path) \
                       --snp genome.snp \
                       --haplotype genome.haplotype \
                       --ss genome.ss \

diff --git a/wdl2cwl/tests/inputs/BuildIndices_mouse.yaml b/wdl2cwl/tests/inputs/BuildIndices_mouse.yaml
@@ -2,4 +2,4 @@ gtf_version: "M21"
 organism: "mouse"
 organism_prefix: "m"
 genome_short_string: "mm10"
-dbsnp_version: "150"
+dbsnp_version: "142"
diff --git a/wdl2cwl/tests/wdl_files/BuildIndices.wdl b/wdl2cwl/tests/wdl_files/BuildIndices.wdl
@@ -23,7 +23,7 @@ task GetReferences {
   String annotation_gtf = "gencode.v~{gtf_version}.primary_assembly.annotation.gtf"
 
   command <<<
-    set -eo pipefail
+    set -exo pipefail
 
     ## download fasta
     wget ~{ftp_path}/~{genome_fa}.gz
@@ -62,7 +62,7 @@ task BuildStar {
   String star_index_name = "~{ref_name}.tar"
 
   command <<<
-    set -eo pipefail
+    set -exo pipefail
 
     mkdir star
     STAR --runMode genomeGenerate \
@@ -105,9 +105,9 @@ task BuildStarSingleNucleus {
   String annotation_gtf_introns = "introns_modified_gencode.v~{gtf_version}.primary_assembly.annotation.gtf"
 
   command <<<
-    set -eo pipefail
+    set -exo pipefail
 
-    /script/modify_gtf_~{organism}.sh ~{references.genome_fa} ~{references.annotation_gtf}
+    bash -ex /script/modify_gtf_~{organism}.sh ~{references.genome_fa} ~{references.annotation_gtf}
 
     mkdir star
     STAR --runMode genomeGenerate \
@@ -254,24 +254,25 @@ task BuildHisat2SnpHaplotypeSplicing {
 
   command <<<
 
+    set -ex
     HISAT2_DIR=/opt/tools/hisat2-2.1.0
 
     # Compressed fasta required here
-    gzip ~{references.genome_fa}
+    gzip ~{references.genome_fa} -c > ~{basename(references.genome_fa)}.gz
 
     # download snp file
     wget http://hgdownload.cse.ucsc.edu/goldenPath/~{genome_short_string}/database/~{snp_file}.gz
     gunzip ~{snp_file}.gz
 
     # extract snps, splice sites, and exon information
-    $HISAT2_DIR/hisat2_extract_snps_UCSC.py ~{references.genome_fa}.gz ~{snp_file} genome
+    $HISAT2_DIR/hisat2_extract_snps_haplotypes_UCSC.py ~{basename(references.genome_fa)}.gz ~{snp_file} genome
     $HISAT2_DIR/hisat2_extract_splice_sites.py ~{references.annotation_gtf} > genome.ss
     $HISAT2_DIR/hisat2_extract_exons.py ~{references.annotation_gtf} > genome.exon
 
     # build the hisat2 reference
     $HISAT2_DIR/hisat2-build \
       -p 8 \
-      genome.fa \
+      ~{references.genome_fa} \
       --snp genome.snp \
       --haplotype genome.haplotype \
       --ss genome.ss \
@@ -331,7 +332,7 @@ task BuildIntervalList {
   String interval_list_name = basename(references.annotation_gtf, ".gtf") + ".interval_list"
 
   command <<<
-    set -eo pipefail
+    set -exo pipefail
 
 
     # index the fasta file