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Add singularity.autoMounts = true to config or put autoMounts = true in scope #48

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FedericoComoglio opened this issue Oct 14, 2019 · 0 comments · Fixed by #53
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Add singularity.autoMounts = true to config or put autoMounts = true in scope #48

FedericoComoglio opened this issue Oct 14, 2019 · 0 comments · Fixed by #53
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@FedericoComoglio
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Hi,

after my sarek runs aborted due to what looked like an issue with singularity autoMounts, I figured this line in nextflow.config

sarek/nextflow.config

Line 118 in 508735e

autoMounts = true

should either be singularity.autoMounts = true or put in a scope.

Hope this helps.
Federico
@maxulysse maxulysse self-assigned this Oct 21, 2019
@maxulysse maxulysse added the bug Something isn't working label Oct 21, 2019
@maxulysse maxulysse mentioned this issue Oct 21, 2019
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maxulysse added a commit that referenced this issue Oct 22, 2019
@maxulysse
fix autoMounts in singularity profile, closes #48
33ff41f
maxulysse added a commit to maxulysse/nf-core_sarek that referenced this issue May 15, 2020
@maxulysse
nf-core bump-version . 2.5.1
8551b2f 
fix script name in docs

fix markdownlint

fix autoMounts in singularity profile, closes nf-core#48

build 2.5.1 version of annotation containers

update CHANGELOG

Typo

Update .github/workflows/branch.yml

Update .github/workflows/branch.yml

Update README.md
maxulysse pushed a commit to maxulysse/nf-core_sarek that referenced this issue May 18, 2020
@maxulysse
added script to help downstream analysis, adding RankScore for Scout
7acb297 
nf-core bump-version . 2.5.1

fix script name in docs

fix markdownlint

fix autoMounts in singularity profile, closes nf-core#48

add patch to branch protection

use correct tag for containers close nf-core#49

update CHANGELOG

Try to fix branch protection

Update README.md

reducing CPU usage for Mpileup

cleanup with meld

some docs additions

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>

added extra space

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>

Update docs/downstream.md

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>

First time CF is working with extra pileups

First working version

Removing nf-core#51 and moving downstream to szilvajuhos/btb-scripts

Fixing some null parameters and C&P typos

yet an other version that somehow worked

remove --normal_pileup and --tumor_pileup params

update freebayes germline command

update changelog

fix --save_bam_mapped + small typos

update CHANGELOG

add step controlfreec

use nf-core header

update config

cleanup

add mappability files to igenomes

better name for tsv file

fix output directory

enable usage of - in names of tools or steps

better default for coefficientofvariation

improve help

update and reorder params

reorder and update params

update and reorder params

update docs

fix prepare_recalibration step

update CHANGELOG

Apply suggestions from code review
maxulysse added a commit to maxulysse/nf-core_sarek that referenced this issue May 18, 2020
@maxulysse
nf-core bump-version . 2.5.1
2ff514b 
fix script name in docs

fix markdownlint

fix autoMounts in singularity profile, closes nf-core#48

build 2.5.1 version of annotation containers

update CHANGELOG

Typo

Update .github/workflows/branch.yml

Update .github/workflows/branch.yml

Update README.md
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Prepare release 2.5.1 maxulysse/nf-core_sarek
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@maxulysse @FedericoComoglio