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To process targeted sequencing with a target BED #635
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added 9 commits
August 16, 2018 11:59
maxulysse
reviewed
Sep 11, 2018
germlineVC.nf
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| concatOptions = "-i ${genomeIndex} -c ${task.cpus} -o ${outputFile} " | ||
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| """ | ||
| ${workflow.projectDir}/scripts/concatenateVCFs.sh ${concatOptions} |
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You should put the new concatenateVCFs.sh script in bin instead, it's directly in the $PATH
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Cool, thanks, I am still testing, but will move
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I noticed that you updated Sarek-data as well, don't forget to update the submodule in Sarek as well |
maxulysse
reviewed
Sep 13, 2018
scripts/wrapper.sh
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| echo "$(tput setaf 1)nextflow run $@ -profile $PROFILE --genome $GENOME --genome_base $GENOMEBASE --tag $TAG --verbose$(tput sgr0) --max_cpus ${CPUS}" | ||
| nextflow run $@ -profile $PROFILE --genome $GENOME --genome_base $GENOMEBASE --tag $TAG --verbose --max_cpus ${CPUS} | ||
| else | ||
| echo "$(tput setaf 1)nextflow run $@ -profile $PROFILE --genome $GENOME --genome_base $GENOMEBASE --tag $TAG --verbose$(tput sgr0) --max_cpus ${CPUS}" --targetBED ${TARGETBED} |
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I think it should be
echo "$(tput setaf 1)nextflow run $@ -profile $PROFILE --genome $GENOME --genome_base $GENOMEBASE --tag $TAG --verbose$(tput sgr0) --max_cpus ${CPUS} --targetBED ${TARGETBED}"
maxulysse
reviewed
Sep 13, 2018
maxulysse
reviewed
Sep 13, 2018
CHANGELOG.md
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| - [#620](https://github.com/SciLifeLab/Sarek/pull/620) - Add `tmp/` to `.gitignore` | ||
| - [#625](https://github.com/SciLifeLab/Sarek/pull/625) - Add [`pathfindr`](https://github.com/NBISweden/pathfindr) as a submodule | ||
| - [#639](https://github.com/SciLifeLab/Sarek/pull/639) - Add a complete example analysis to docs | ||
| - [#629](https://github.com/SciLifeLab/Sarek/pull/629) - Add a complete example analysis to docs |
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Actually this one really was the #639
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It has not to be the PR name.
It could be a shorter description, since a PR can fall into Added, Changed, Removedor evenFixedcategory at the same time. For meAddedis anything new andChanged` is anything updated
added 2 commits
September 21, 2018 09:59
maxulysse
reviewed
Sep 21, 2018
maxulysse
reviewed
Sep 21, 2018
jherrero
referenced
this pull request
in UCL-BLIC/Sarek_v2.2.1
Apr 11, 2019
To process targeted sequencing with a target BED
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Changes to make possible to add a BED file and run targeted processing for both germline and somatic calls. To be tested on real WES data.
PR checklist
devbranchmasterbranch./scripts/test.sh -p docker -t ALL).docsis updatedCHANGELOG.mdis updatedREADME.mdis updatedLearn more about contributing: https://github.com/SciLifeLab/Sarek/blob/master/.github/CONTRIBUTING.md