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zavolan_group
pipelines
ZARP
Commits
b62f3bf1
Commit
b62f3bf1
authored
4 years ago
by
BIOPZ-Gypas Foivos
Committed by
Alex Kanitz
4 years ago
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refactor: use zgtf for GTF to BED12 conversion
parent
4dd1ad78
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1 merge request
!76
Bump version to v0.2.0
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.gitlab-ci.yml
+2
-2
2 additions, 2 deletions
.gitlab-ci.yml
Snakefile
+9
-5
9 additions, 5 deletions
Snakefile
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11 additions
and
7 deletions
.gitlab-ci.yml
+
2
−
2
View file @
b62f3bf1
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@@ -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
...
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Snakefile
+
9
−
5
View file @
b62f3bf1
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@@ -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/
z
gtf
: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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