Merge pull request #5 from dbmi-bgm/fix_preprocess_name

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dbmi-bgm · Aug 22, 2022 · 94142c9 · 94142c9
2 parents 66cde7d + 32e48a6
commit 94142c9
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Showing 8 changed files with 5 additions and 6 deletions.
diff --git a/cwl/preprocess_liftover.cwl b/cwl/preprocess_liftover.cwl
@@ -9,15 +9,15 @@ requirements:
 
 hints:
   - class: DockerRequirement
-    dockerPull: ACCOUNT/granite_preprocess_liftover:VERSION
+    dockerPull: ACCOUNT/granite:VERSION
 
 baseCommand: [python3, /usr/local/bin/preprocess_liftover.py]
 
 inputs:
   - id: vcf
     type: File
     inputBinding:
-      prefix: -i 
+      prefix: -i
     doc: expect a path to the input uncompressed or gzip-compressed vcf
 
   - id: sample_names
@@ -26,7 +26,7 @@ inputs:
         prefix: -s
     doc: list of sample IDs
 
-  - id: output_vcf 
+  - id: output_vcf
     type: string
     default: "output.vcf"
     inputBinding:
@@ -41,4 +41,3 @@ outputs:
 
 doc: |
     run preprocess_liftover.py to validate input VCF file for the liftover step
-
diff --git a/...es/granite_preprocess_liftover/Dockerfile → dockerfiles/granite/Dockerfile b/...es/granite_preprocess_liftover/Dockerfile → dockerfiles/granite/Dockerfile
diff --git a/...s_liftover/scripts/preprocess_liftover.py → ...es/granite/scripts/preprocess_liftover.py b/...s_liftover/scripts/preprocess_liftover.py → ...es/granite/scripts/preprocess_liftover.py
@@ -4,8 +4,8 @@
 #
 #       Script to validate input VCF file for the liftover step.
 #       It runs the following steps:
-#       1. Check if sample identifiers in the VCF matches provided sample names
-#       2. Exlcude non standard chromosomes i.e GL000225.1
+#       1. Check if sample identifiers in the VCF match provided sample names
+#       2. Exclude non standard chromosomes i.e GL000225.1
 #       3. If the VCF is not 'chr' based, add the prefix
 #
 ##################################################################################

diff --git a/.../files/liftover_vcf_chr_missing_in.vcf.gz → .../files/liftover_vcf_chr_missing_in.vcf.gz b/.../files/liftover_vcf_chr_missing_in.vcf.gz → .../files/liftover_vcf_chr_missing_in.vcf.gz
diff --git a/...s/test/files/liftover_vcf_correct_out.vcf → ...s/test/files/liftover_vcf_correct_out.vcf b/...s/test/files/liftover_vcf_correct_out.vcf → ...s/test/files/liftover_vcf_correct_out.vcf
diff --git a/...liftover_vcf_non_standard_chrom_in.vcf.gz → ...liftover_vcf_non_standard_chrom_in.vcf.gz b/...liftover_vcf_non_standard_chrom_in.vcf.gz → ...liftover_vcf_non_standard_chrom_in.vcf.gz
diff --git a/.../files/liftover_vcf_two_samples_in.vcf.gz → .../files/liftover_vcf_two_samples_in.vcf.gz b/.../files/liftover_vcf_two_samples_in.vcf.gz → .../files/liftover_vcf_two_samples_in.vcf.gz
diff --git a/.../scripts/test/test_preprocess_liftover.py → .../scripts/test/test_preprocess_liftover.py b/.../scripts/test/test_preprocess_liftover.py → .../scripts/test/test_preprocess_liftover.py