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Change report generation call #161

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merged 6 commits into from
Jan 21, 2021
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@boulund boulund commented Jan 20, 2021

Ignore additional arguments to snakemake when creating report,

Intended to avoid shell escaping issue with complex arguments to e.g. Singularity, issue #160

Ignore additional arguments to snakemake when creating report,

Intended to avoid shell escaping issue with complex arguments to e.g. Singularity, issue #160
@boulund boulund requested a review from AroArz January 20, 2021 14:05
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AroArz commented Jan 20, 2021

Did you have a chance to test this?

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boulund commented Jan 20, 2021

Haha. Not at all, just made the changes in the github web editor. Don't have an opportunity to test this today.

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Okay so apparently snakemake_call returns the entire path to snakemake like /home/aroarz/miniconda3/bin/snakemake --use-singularity --singularity-args -B /proj/snic2020-6-233/db.

Which means snakemake_call[0] returns /, still producing an error.

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boulund commented Jan 21, 2021

Did you test it already? You're so quick!
If you're confident it works better than earlier we can make a note about it in the changelog (something like "Implemented workaround for automatic report generation when using Singularity")?

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AroArz commented Jan 21, 2021

Yes! I tested all the changes, I also added the bit to the changelog

AroArz and others added 3 commits January 21, 2021 12:16
Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com>
Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com>
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boulund commented Jan 21, 2021

Awesome!

@boulund boulund merged commit 7434132 into develop Jan 21, 2021
boulund added a commit that referenced this pull request Feb 2, 2021
* Update version to 0.4.1-dev

* Update CircleCI badge in README to monitor develop branch

* Add Singularity deffile for stag-mwc env

* Add Singularity image for main env up to kraken2

* Add link to Singularity bind docs

* Add stag-mwc-main singularity image to all rules that require it

* Add Singularity images for biobakery and assembly

* Set rule threads from cluster_config if defined

* Update CHANGELOG

* Docs: Update module intro paragraph, closes #151

* Add {cluster.extra} to slurm-submit.py script call

* Update CHANGELOG

* Fix typo in kraken2 rules

* the host removal script was ignoring it's flag in config.yaml

* Update CHANGELOG

* Update CHANGELOG

* Tweak docs, update changelog, prepare for release

* Amrplusplus (#156)

* amrplusplus

* amrplusplus scripts

* added scripts

* changed input in config.yaml

Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com>

* default db empty

Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com>

* db -> megares

Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com>

* annotation --> megares_annotation

Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com>

* added amrplusplus to circleci

* updated CHANGELOG.md

* updated amrplusplus in config.yaml

* added amrplusplus to modules.rst

* updated amrplusplus.smk

* added license and removed bin dir

* updated modules.rst

* added align_to_amr

* fixed default database

* amrplusplus db empty in conf

* indentations

* clarification regarding database

* Update docs/source/modules.rst

Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com>

* Update rules/antibiotic_resistance/amrplusplus.smk

Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com>

* Update docs/source/modules.rst grammar

Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com>

* Update CHANGELOG.md

Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com>

* added bwa to stag-mwc.yaml

* added conda environment

* amrplusplus exectuable with conda

* amrplusplus executable with conda

* samtools version 1.10

* amrplusplus conda executable

* added amrplusplus.yaml to not break stag-mwc.yaml dependencies

* removed amrplusplus dependencies because they broke it

* now using amrplusplus.yaml for conda instead of stag-mwc.yaml

Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com>
Co-authored-by: Aron Arzoomand <aron@debian.ki.se>

* Change report generation call (#161)

* Change report generation call

Ignore additional arguments to snakemake when creating report,

Intended to avoid shell escaping issue with complex arguments to e.g. Singularity, issue #160

* removed snakemake_call

* added report generation workaround

* report generation

Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com>

* report generation

Co-authored-by: Fredrik Boulund <boulund@users.noreply.github.com>

* indentation

Co-authored-by: Aron Arzoomand <51719360+AroArz@users.noreply.github.com>

* Slurm profile for CTMR UCP environment (#159)

* First draft for CTMR UCP cluster profile

* Remove references to rackham profile, remove account check

* Updated resource requests for all rules

* Final tweaks

* Rename ctmr_ucp profile to ctmr_gandalf

* Fix yml-yaml typo

* Fix incorrectly named singularity images

* Remove --use prefix for argument to metawrap

* Add missing singularity container to create_kaiju_krona_plot

* added dbdir and threads for align_to_amr

* Disable area plot for Kaiju

* Minor updates to docs (#162)

* Update badge URL in README

Co-authored-by: Kristaps <kbebris@gmail.com>
Co-authored-by: Aron Arzoomand <51719360+AroArz@users.noreply.github.com>
Co-authored-by: Aron Arzoomand <aron@debian.ki.se>
Co-authored-by: AroArz <aron_arzoomand@live.se>
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2 participants