Minor updates to docs #162
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* 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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