From 3e14c55e52b0f0a9a2b4e2db5353cb1e7b121c14 Mon Sep 17 00:00:00 2001 From: "41898282+github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 25 Nov 2024 14:03:49 +0000 Subject: [PATCH] Deployed 4f486a5 to 0.11 with MkDocs 1.6.1 and mike 2.1.3 --- 0.11/404.html | 2 +- 0.11/CHANGELOG/index.html | 2 +- .../assets/javascripts/bundle.56dfad97.min.js | 16 ----- .../assets/javascripts/bundle.83f73b43.min.js | 16 +++++ ....min.js.map => bundle.83f73b43.min.js.map} | 8 +-- ...07f07601.min.js => search.6ce7567c.min.js} | 6 +- ....min.js.map => search.6ce7567c.min.js.map} | 4 +- 0.11/assets/stylesheets/main.35f28582.min.css | 1 - .../stylesheets/main.35f28582.min.css.map | 1 - 0.11/assets/stylesheets/main.6f8fc17f.min.css | 1 + .../stylesheets/main.6f8fc17f.min.css.map | 1 + 0.11/contributing/index.html | 4 +- 0.11/flowchart/index.html | 2 +- 0.11/index.html | 34 +++++----- 0.11/platforms/index.html | 4 +- 0.11/references/index.html | 4 +- 0.11/search/search_index.json | 2 +- 0.11/sitemap.xml.gz | Bin 127 -> 127 bytes 0.11/tutorial/index.html | 60 +++++++----------- 19 files changed, 79 insertions(+), 89 deletions(-) delete mode 100644 0.11/assets/javascripts/bundle.56dfad97.min.js create mode 100644 0.11/assets/javascripts/bundle.83f73b43.min.js rename 0.11/assets/javascripts/{bundle.56dfad97.min.js.map => bundle.83f73b43.min.js.map} (71%) rename 0.11/assets/javascripts/workers/{search.07f07601.min.js => search.6ce7567c.min.js} (94%) rename 0.11/assets/javascripts/workers/{search.07f07601.min.js.map => search.6ce7567c.min.js.map} (78%) delete mode 100644 0.11/assets/stylesheets/main.35f28582.min.css delete mode 100644 0.11/assets/stylesheets/main.35f28582.min.css.map create mode 100644 0.11/assets/stylesheets/main.6f8fc17f.min.css create mode 100644 0.11/assets/stylesheets/main.6f8fc17f.min.css.map diff --git a/0.11/404.html b/0.11/404.html index 0e58516..504b5e0 100644 --- a/0.11/404.html +++ b/0.11/404.html @@ -1 +1 @@ -
TEMPDIR
in the config file sets the temporary directory location for rules that require transient storage.--singcache
argument to provide a singularity cache dir location. The singularity cache dir is automatically set inside /data/$USER/
or $WORKDIR/
if --singcache
is not provided.Significant upgrades since the last release:
cutadapt_min_length to cutadapt rule... setting it to 15 in config (for miRNAs, Biot and short viral features)
run_clear
is now set to True (as default)circ_quant
replaces clear_quant
in the CLEAR rule. In order words, we are reusing the STAR alignment file and the circExplorer2 output file for running CLEAR. No need to run HISAT2 and TopHat (fusion-search with Bowtie1). This is much quicker.WORKDIR
can now be a relative pathrun_circrna_daq.sh
) added for local and cluster execution.envmodules
used in Snakemake in place of module load
statements$PYTHONPATH
. (#119, #125, @kelly-sovacool)-C
.python -E
to ensure the $PYTHONPATH
is not carried over. (#129, @kelly-sovacool)reconfig
to correctly replace variables in the config file. (#121, @kelly-sovacool)TEMPDIR
in the config file sets the temporary directory location for rules that require transient storage.--singcache
argument to provide a singularity cache dir location. The singularity cache dir is automatically set inside /data/$USER/
or $WORKDIR/
if --singcache
is not provided.Significant upgrades since the last release:
cutadapt_min_length to cutadapt rule... setting it to 15 in config (for miRNAs, Biot and short viral features)
run_clear
is now set to True (as default)circ_quant
replaces clear_quant
in the CLEAR rule. In order words, we are reusing the STAR alignment file and the circExplorer2 output file for running CLEAR. No need to run HISAT2 and TopHat (fusion-search with Bowtie1). This is much quicker.WORKDIR
can now be a relative pathrun_circrna_daq.sh
) added for local and cluster execution.envmodules
used in Snakemake in place of module load
statements