fix: tests and bugs and CI (#187)

* chore: mv tests/tools/input to tests/input * fix: update test paths * revise: rename star_db to include contigs * WIP * Update star.wdl * WIP * WIP * fix: only grep for RG at start of line * fix: update paths * revise: rename things * WIP * WIP * fix: * fix * Update test_fastqc.yaml * Update test_fastqc.yaml * Update multiqc.json * fix: more renaming * Update test_samtools.py * Update test_util.yaml * Update test_picard.yaml * Update test_picard.yaml * Update lint-check.yaml * fix: bump to latest util image * chore: don't use branch image
stjudecloud · Nov 26, 2024 · 43462b0 · 43462b0
1 parent 75a640b
commit 43462b0
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diff --git a/.github/workflows/lint-check.yaml b/.github/workflows/lint-check.yaml
@@ -71,6 +71,6 @@ jobs:
                 EXITCODE=2
                 ;;
             esac
-          done < <(awk '/docker: .*stjudecloud/' < "$file")
+          done < <(awk '/container: .*stjudecloud/' < "$file")
         done
         exit $EXITCODE
diff --git a/.gitignore b/.gitignore
@@ -12,9 +12,12 @@
 *.jar
 miniwdl_call_cache/
 miniwdl_singularity_cache/
+_LAST
+202*/
 
 # Blacklist test directories
 test-output/
+**/__pycache__
 
 # Blacklist OS generated files
 .DS_Store

diff --git a/data_structures/flag_filter.wdl b/data_structures/flag_filter.wdl
@@ -118,7 +118,7 @@ task validate_string_is_12bit_oct_dec_or_hex {
     runtime {
         memory: "4 GB"
         disks: "10 GB"
-        container: "ghcr.io/stjudecloud/util:1.3.0"
+        container: "ghcr.io/stjudecloud/util:1.4.0"
         maxRetries: 1
     }
 }

diff --git a/docker/STAR/2.7.11b-0/Dockerfile → docker/STAR/2.7.11b-1/Dockerfile b/docker/STAR/2.7.11b-0/Dockerfile → docker/STAR/2.7.11b-1/Dockerfile
@@ -4,7 +4,7 @@ RUN apt-get update \
     && apt-get --yes install --no-install-recommends python3 \
     && rm -rf /var/lib/apt/lists/*
 
-FROM quay.io/biocontainers/star:2.7.11b--h43eeafb_0
+FROM quay.io/biocontainers/star:2.7.11b--h43eeafb_3
 
 COPY --from=python /lib/x86_64-linux-gnu/libexpat.so.1 /lib/x86_64-linux-gnu/
 COPY --from=python /lib/x86_64-linux-gnu/libz.so.1 /lib/x86_64-linux-gnu/

diff --git a/docker/STAR/2.7.11b-0/sort_star_input.py → docker/STAR/2.7.11b-1/sort_star_input.py b/docker/STAR/2.7.11b-0/sort_star_input.py → docker/STAR/2.7.11b-1/sort_star_input.py
diff --git a/tests/tools/input/1scattered.interval_list → tests/input/1scattered.interval_list b/tests/tools/input/1scattered.interval_list → tests/input/1scattered.interval_list
diff --git a/tests/input/Aligned.sortedByCoord.chr9_chr22.bam b/tests/input/Aligned.sortedByCoord.chr9_chr22.bam
diff --git a/tests/input/Aligned.sortedByCoord.chr9_chr22.bam.bai b/tests/input/Aligned.sortedByCoord.chr9_chr22.bam.bai
diff --git a/tests/tools/input/GRCh38.chr1_chr19.dict → tests/input/GRCh38.chr1_chr19.dict b/tests/tools/input/GRCh38.chr1_chr19.dict → tests/input/GRCh38.chr1_chr19.dict
diff --git a/tests/tools/input/GRCh38.chr1_chr19.fa → tests/input/GRCh38.chr1_chr19.fa b/tests/tools/input/GRCh38.chr1_chr19.fa → tests/input/GRCh38.chr1_chr19.fa
diff --git a/tests/tools/input/GRCh38.chr1_chr19.fa.fai → tests/input/GRCh38.chr1_chr19.fa.fai b/tests/tools/input/GRCh38.chr1_chr19.fa.fai → tests/input/GRCh38.chr1_chr19.fa.fai
diff --git a/tests/tools/input/GRCh38.chr9_chr22.fa.gz → tests/input/GRCh38.chr9_chr22.fa.gz b/tests/tools/input/GRCh38.chr9_chr22.fa.gz → tests/input/GRCh38.chr9_chr22.fa.gz
diff --git a/tests/input/GRCh38.chrY_chrM.dict b/tests/input/GRCh38.chrY_chrM.dict
@@ -0,0 +1,3 @@
+@HD	VN:1.0	SO:unsorted
+@SQ	SN:chrY	LN:57227415	M5:ce3e31103314a704255f3cd90369ecce	UR:file:///Users/afrantz/workflows/tests/input/GRCh38.chrY_chrM.fa.gz
+@SQ	SN:chrM	LN:16569	M5:c68f52674c9fb33aef52dcf399755519	UR:file:///Users/afrantz/workflows/tests/input/GRCh38.chrY_chrM.fa.gz
diff --git a/tests/input/GRCh38.chrY_chrM.fa b/tests/input/GRCh38.chrY_chrM.fa
diff --git a/tests/input/GRCh38.chrY_chrM.fa.fai b/tests/input/GRCh38.chrY_chrM.fa.fai
@@ -0,0 +1,2 @@
+chrY	57227415	147	70	71
+chrM	16569	58045219	70	71
diff --git a/tests/tools/input/GRCh38.tar.gz → tests/input/GRCh38.tar.gz b/tests/tools/input/GRCh38.tar.gz → tests/input/GRCh38.tar.gz
diff --git a/...o_sapiens_assembly38.dbsnp138.top5000.vcf → ...o_sapiens_assembly38.dbsnp138.top5000.vcf b/...o_sapiens_assembly38.dbsnp138.top5000.vcf → ...o_sapiens_assembly38.dbsnp138.top5000.vcf
diff --git a/...piens_assembly38.dbsnp138.top5000.vcf.idx → ...piens_assembly38.dbsnp138.top5000.vcf.idx b/...piens_assembly38.dbsnp138.top5000.vcf.idx → ...piens_assembly38.dbsnp138.top5000.vcf.idx
diff --git a/...nd_1000G_gold_standard.indels.hg38.vcf.gz → ...nd_1000G_gold_standard.indels.hg38.vcf.gz b/...nd_1000G_gold_standard.indels.hg38.vcf.gz → ...nd_1000G_gold_standard.indels.hg38.vcf.gz
diff --git a/...000G_gold_standard.indels.hg38.vcf.gz.tbi → ...000G_gold_standard.indels.hg38.vcf.gz.tbi b/...000G_gold_standard.indels.hg38.vcf.gz.tbi → ...000G_gold_standard.indels.hg38.vcf.gz.tbi
diff --git a/.../input/SJBT031344_D1.Exome.multiqc.tar.gz → .../input/SJBT031344_D1.Exome.multiqc.tar.gz b/.../input/SJBT031344_D1.Exome.multiqc.tar.gz → .../input/SJBT031344_D1.Exome.multiqc.tar.gz
diff --git a/tests/tools/input/bwa_db.tar.gz → tests/input/bwa_db.tar.gz b/tests/tools/input/bwa_db.tar.gz → tests/input/bwa_db.tar.gz
diff --git a/tests/tools/input/chr1.interval_list → tests/input/chr1.interval_list b/tests/tools/input/chr1.interval_list → tests/input/chr1.interval_list
diff --git a/tests/tools/input/fusions.tsv → tests/input/fusions.tsv b/tests/tools/input/fusions.tsv → tests/input/fusions.tsv
diff --git a/...tools/input/gencode.v31.chr9_chr22.gtf.gz → tests/input/gencode.v31.chr9_chr22.gtf.gz b/...tools/input/gencode.v31.chr9_chr22.gtf.gz → tests/input/gencode.v31.chr9_chr22.gtf.gz
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		chrY 57227415 147 70 71
		chrM 16569 58045219 70 71