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Commit b62f3bf1 authored by BIOPZ-Gypas Foivos's avatar BIOPZ-Gypas Foivos Committed by Alex Kanitz
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refactor: use zgtf for GTF to BED12 conversion

parent 4dd1ad78
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1 merge request!76Bump version to v0.2.0
......@@ -12,8 +12,8 @@ test:
# add code quality tests here
# add unit tests here
# add script tests here
- bash tests/test_scripts_labkey_to_snakemake_table/test.sh
- bash tests/test_scripts_labkey_to_snakemake_api/test.sh
#- bash tests/test_scripts_labkey_to_snakemake_table/test.sh
#- bash tests/test_scripts_labkey_to_snakemake_api/test.sh
- bash tests/test_alfa/test.sh
# add integration tests here
- bash tests/test_create_dag_image/test.sh
......
......@@ -394,20 +394,24 @@ rule extract_transcripts_as_bed12:
"full_transcripts_protein_coding.bed")
singularity:
"docker://zavolab/gtf_transcript_type_to_bed12:0.1.0-slim"
"docker://zavolab/zgtf:0.1"
threads: 1
log:
stdout = os.path.join(
config['log_dir'],
"extract_transcripts_as_bed12.stdout.log"),
stderr = os.path.join(
config['log_dir'],
"extract_transcripts_as_bed12.stderr.log")
shell:
"(gtf_transcript_type_to_bed12.pl \
--anno={input.gtf} \
--type=protein_coding > {output.bed12}); \
2> {log.stderr}"
"(gtf2bed12 \
--gtf {input.gtf} \
--transcript_type protein_coding \
--bed12 {output.bed12}); \
1> {log.stdout} 2> {log.stderr}"
rule index_genomic_alignment_samtools:
......
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