diff --git a/cwl/preprocess_liftover.cwl b/cwl/preprocess_liftover.cwl index cf194f9..cd09314 100644 --- a/cwl/preprocess_liftover.cwl +++ b/cwl/preprocess_liftover.cwl @@ -9,7 +9,7 @@ requirements: hints: - class: DockerRequirement - dockerPull: ACCOUNT/granite_preprocess_liftover:VERSION + dockerPull: ACCOUNT/granite:VERSION baseCommand: [python3, /usr/local/bin/preprocess_liftover.py] @@ -17,7 +17,7 @@ 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/dockerfiles/granite_preprocess_liftover/Dockerfile b/dockerfiles/granite/Dockerfile similarity index 100% rename from dockerfiles/granite_preprocess_liftover/Dockerfile rename to dockerfiles/granite/Dockerfile diff --git a/dockerfiles/granite_preprocess_liftover/scripts/preprocess_liftover.py b/dockerfiles/granite/scripts/preprocess_liftover.py similarity index 94% rename from dockerfiles/granite_preprocess_liftover/scripts/preprocess_liftover.py rename to dockerfiles/granite/scripts/preprocess_liftover.py index 2c01e9b..b933da7 100644 --- a/dockerfiles/granite_preprocess_liftover/scripts/preprocess_liftover.py +++ b/dockerfiles/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/dockerfiles/granite_preprocess_liftover/scripts/test/files/liftover_vcf_chr_missing_in.vcf.gz b/dockerfiles/granite/scripts/test/files/liftover_vcf_chr_missing_in.vcf.gz similarity index 100% rename from dockerfiles/granite_preprocess_liftover/scripts/test/files/liftover_vcf_chr_missing_in.vcf.gz rename to dockerfiles/granite/scripts/test/files/liftover_vcf_chr_missing_in.vcf.gz diff --git a/dockerfiles/granite_preprocess_liftover/scripts/test/files/liftover_vcf_correct_out.vcf b/dockerfiles/granite/scripts/test/files/liftover_vcf_correct_out.vcf similarity index 100% rename from dockerfiles/granite_preprocess_liftover/scripts/test/files/liftover_vcf_correct_out.vcf rename to dockerfiles/granite/scripts/test/files/liftover_vcf_correct_out.vcf diff --git a/dockerfiles/granite_preprocess_liftover/scripts/test/files/liftover_vcf_non_standard_chrom_in.vcf.gz b/dockerfiles/granite/scripts/test/files/liftover_vcf_non_standard_chrom_in.vcf.gz similarity index 100% rename from dockerfiles/granite_preprocess_liftover/scripts/test/files/liftover_vcf_non_standard_chrom_in.vcf.gz rename to dockerfiles/granite/scripts/test/files/liftover_vcf_non_standard_chrom_in.vcf.gz diff --git a/dockerfiles/granite_preprocess_liftover/scripts/test/files/liftover_vcf_two_samples_in.vcf.gz b/dockerfiles/granite/scripts/test/files/liftover_vcf_two_samples_in.vcf.gz similarity index 100% rename from dockerfiles/granite_preprocess_liftover/scripts/test/files/liftover_vcf_two_samples_in.vcf.gz rename to dockerfiles/granite/scripts/test/files/liftover_vcf_two_samples_in.vcf.gz diff --git a/dockerfiles/granite_preprocess_liftover/scripts/test/test_preprocess_liftover.py b/dockerfiles/granite/scripts/test/test_preprocess_liftover.py similarity index 100% rename from dockerfiles/granite_preprocess_liftover/scripts/test/test_preprocess_liftover.py rename to dockerfiles/granite/scripts/test/test_preprocess_liftover.py