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Commit ec949139 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Merge branch 'update.containers' into 'develop' 

Update.containers

See merge request !72
parents f8e44f43 e3366771
3 merge requests!76Develop,!74Develop,!72Update.containers
Pipeline #9539 passed with stages
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.gitlab-ci.yml
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......@@ -33,7 +33,7 @@ img_cache:
stage: singularity
script:
- mkdir -p ${dir}cache/
- cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | xargs -P 3 -I {} bash -c "singularity pull --dir ${dir} 'docker://'{} || true"
- cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | xargs -P 1 -I {} bash -c "singularity pull --dir ${dir} 'docker://'{} || true"
- wait
- echo images cached
......
CHANGELOG.md
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......@@ -9,6 +9,7 @@
* Modify repository structure to allow for use with XPACK-DNANEXUS
* Add override for endness
* Add seqtk to references
* Update software versions to latest (containers)
**Background**
* Add memory limit (75%) per thread for samtools sort (#108)
......
docs/software_references_mqc.yaml
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− 12
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......@@ -25,49 +25,49 @@
<ul>
<li>D'Arcy, M., Chard, K., Foster, I., Kesselman, C., Madduri, R., Saint, N., &amp; Wagner, R.. 2019. Big Data Bags: A Scalable Packaging Format for Science. Zenodo. doi:<a href="http://doi.org/10.5281/zenodo.3338725">10.5281/zenodo.3338725</a>.</li>
</ul>
<ol start="5" style="list-style-type: decimal">
<ol start="4" style="list-style-type: decimal">
<li><strong>trimgalore</strong>:</li>
</ol>
<ul>
<li>trimgalore <a href="https://github.com/FelixKrueger/TrimGalore" class="uri">https://github.com/FelixKrueger/TrimGalore</a></li>
</ul>
<ol start="6" style="list-style-type: decimal">
<ol start="5" style="list-style-type: decimal">
<li><strong>hisat2</strong>:</li>
</ol>
<ul>
<li>Kim ,D.,Paggi, J.M., Park, C., Bennett, C., Salzberg, S.L. 2019 Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. Aug;37(8):907-915. doi:<a href="https://doi.org/10.1038/s41587-019-0201-4">10.1038/s41587-019-0201-4</a>.</li>
</ul>
<ol start="7" style="list-style-type: decimal">
<ol start="6" style="list-style-type: decimal">
<li><strong>samtools</strong>:</li>
</ol>
<ul>
<li>Li H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin, and 1000 Genome Project Data Processing Subgroup. 2009. The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25: 2078-9. doi:<a href="http://dx.doi.org/10.1093/bioinformatics/btp352">10.1093/bioinformatics/btp352</a></li>
</ul>
<ol start="8" style="list-style-type: decimal">
<ol start="7" style="list-style-type: decimal">
<li><strong>picard</strong>:</li>
</ol>
<ul>
<li>“Picard Toolkit.” 2019. Broad Institute, GitHub Repository. <a href="http://broadinstitute.github.io/picard/" class="uri">http://broadinstitute.github.io/picard/</a>; Broad Institute</li>
</ul>
<ol start="9" style="list-style-type: decimal">
<ol start="8" style="list-style-type: decimal">
<li><strong>featureCounts</strong>:</li>
</ol>
<ul>
<li>Liao, Y., Smyth, G.K., Shi, W. 2014 featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. Apr 1;30(7):923-30. doi:<a href="https://doi.org/10.1093/bioinformatics/btt656">10.1093/bioinformatics/btt656</a>.</li>
</ul>
<ol start="11" style="list-style-type: decimal">
<ol start="9" style="list-style-type: decimal">
<li><strong>deeptools</strong>:</li>
</ol>
<ul>
<li>Ramírez, F., D. P. Ryan, B. Grüning, V. Bhardwaj, F. Kilpert, A. S. Richter, S. Heyne, F. Dündar, and T. Manke. 2016. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Research 44: W160-165. doi:<a href="http://dx.doi.org/10.1093/nar/gkw257">10.1093/nar/gkw257</a></li>
</ul>
<ol start="11" style="list-style-type: decimal">
<ol start="10" style="list-style-type: decimal">
<li><strong>Seqtk</strong>:</li>
</ol>
<ul>
<li>Seqtk <a href="https://github.com/lh3/seqtk" class="uri">https://github.com/lh3/seqtk</a></li>
</ul>
<ol start="10" style="list-style-type: decimal">
<ol start="11" style="list-style-type: decimal">
<li><strong>R</strong>:</li>
</ol>
<ul>
......@@ -79,25 +79,25 @@
<ul>
<li>FastQC <a href="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/" class="uri">https://www.bioinformatics.babraham.ac.uk/projects/fastqc/</a></li>
</ul>
<ol start="12" style="list-style-type: decimal">
<ol start="13" style="list-style-type: decimal">
<li><strong>SeqWho</strong></li>
</ol>
<ul>
<li>SeqWho <a href="https://git.biohpc.swmed.edu/s181649/seqwho" class="uri">https://git.biohpc.swmed.edu/s181649/seqwho</a></li>
</ul>
<ol start="4" style="list-style-type: decimal">
<ol start="14" style="list-style-type: decimal">
<li><strong>RSeQC</strong>:</li>
</ol>
<ul>
<li>Wang, L., Wang, S., Li, W. 2012 RSeQC: quality control of RNA-seq experiments. Bioinformatics. Aug 15;28(16):2184-5. doi:<a href="https://doi.org/10.1093/bioinformatics/bts356">10.1093/bioinformatics/bts356</a>.</li>
</ul>
<ol start="13" style="list-style-type: decimal">
<ol start="15" style="list-style-type: decimal">
<li><strong>MultiQC</strong>:</li>
</ol>
<ul>
<li>Ewels P., Magnusson M., Lundin S. and Käller M. 2016. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19): 3047–3048. doi:<a href="https://dx.doi.org/10.1093/bioinformatics/btw354">10.1093/bioinformatics/btw354</a></li>
</ul>
<ol start="14" style="list-style-type: decimal">
<ol start="16" style="list-style-type: decimal">
<li><strong>Nextflow</strong>:</li>
</ol>
<ul>
......
docs/software_versions_mqc.yaml
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......@@ -7,20 +7,20 @@
data: |
<dl class="dl-horizontal">
<dt>Python</dt><dd>v3.8.3</dd>
<dt>DERIVA</dt><dd>v1.4.3</dd>
<dt>BDBag</dt><dd>v1.5.6</dd>
<dt>Trim Galore!</dt><dd>v0.6.4_dev</dd>
<dt>Python</dt><dd>v3.8.5</dd>
<dt>DERIVA</dt><dd>v1.4.5</dd>
<dt>BDBag</dt><dd>v1.6.0</dd>
<dt>Trim Galore!</dt><dd>v0.6.6</dd>
<dt>HISAT2</dt><dd>v2.2.1</dd>
<dt>Samtools</dt><dd>v1.11</dd>
<dt>picard (MarkDuplicates)</dt><dd>v2.23.9</dd>
<dt>picard (MarkDuplicates)</dt><dd>v2.25.0</dd>
<dt>featureCounts</dt><dd>v2.0.1</dd>
<dt>deepTools</dt><dd>v3.5.0</dd>
<dt>Seqtk</dt><dd>v1.3-r106</dd>
<dt>R</dt><dd>v4.0.3</dd>
<dt>R</dt><dd>v4.0.4</dd>
<dt>FastQC</dt><dd>v0.11.9</dd>
<dt>SeqWho</dt><dd>vBeta-1.0.0</dd>
<dt>RSeQC</dt><dd>v4.0.0</dd>
<dt>MultiQC</dt><dd>v1.9</dd>
<dt>MultiQC</dt><dd>v1.10</dd>
<dt>Pipeline Version</dt><dd>v2.0.0rc01</dd>
</dl>
nextflow.config
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View file @ ec949139
......@@ -23,91 +23,91 @@ profiles {
process {
withName:trackStart {
container = 'gudmaprbk/gudmap-rbk_base:1.0.0'
container = 'gudmaprbk/gudmap-rbk_base:1.0.1'
}
withName:getBag {
container = 'gudmaprbk/deriva1.4:1.0.0'
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:getData {
container = 'gudmaprbk/deriva1.4:1.0.0'
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:parseMetadata {
container = 'gudmaprbk/python3:1.0.0'
container = 'gudmaprbk/python3:1.0.1'
}
withName:getRefERCC {
container = 'gudmaprbk/deriva1.4:1.0.0'
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:getRef {
container = 'gudmaprbk/deriva1.4:1.0.0'
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:fastqc {
container = 'gudmaprbk/fastqc0.11.9:1.0.0'
container = 'gudmaprbk/fastqc0.11.9:1.0.1'
}
withName:seqwho {
container = 'gudmaprbk/seqwho0.0.1:1.0.0'
}
withName:trimData {
container = 'gudmaprbk/trimgalore0.6.5:1.0.0'
container = 'gudmaprbk/trimgalore0.6.6:1.0.0'
}
withName:downsampleData {
container = 'gudmaprbk/seqtk1.3:1.0.0'
container = 'gudmaprbk/seqtk1.3:1.0.1'
}
withName:alignSampleDataERCC {
container = 'gudmaprbk/hisat2.2.1:1.0.0'
container = 'gudmaprbk/hisat2.2.1:1.0.1'
}
withName:alignSampleData {
container = 'gudmaprbk/hisat2.2.1:1.0.0'
container = 'gudmaprbk/hisat2.2.1:1.0.1'
}
withName:inferMetadata {
container = 'gudmaprbk/rseqc4.0.0:1.0.0'
container = 'gudmaprbk/rseqc4.0.0:1.0.1'
}
withName:checkMetadata {
container = 'gudmaprbk/gudmap-rbk_base:1.0.0'
container = 'gudmaprbk/gudmap-rbk_base:1.0.1'
}
withName:alignData {
container = 'gudmaprbk/hisat2.2.1:1.0.0'
container = 'gudmaprbk/hisat2.2.1:1.0.1'
}
withName:dedupData {
container = 'gudmaprbk/picard2.23.9:1.0.0'
container = 'gudmaprbk/picard2.25.0:1.0.0'
}
withName:countData {
container = 'gudmaprbk/subread2.0.1:1.0.0'
container = 'gudmaprbk/subread2.0.1:1.0.1'
}
withName:makeBigWig {
container = 'gudmaprbk/deeptools3.5.0:1.0.0'
container = 'gudmaprbk/deeptools3.5.0:1.0.1'
}
withName:dataQC {
container = 'gudmaprbk/rseqc4.0.0:1.0.0'
container = 'gudmaprbk/rseqc4.0.0:1.0.1'
}
withName:aggrQC {
container = 'gudmaprbk/multiqc1.9:1.0.0'
container = 'gudmaprbk/multiqc1.10:1.0.0'
}
withName:uploadInputBag {
container = 'gudmaprbk/deriva1.4:1.0.0'
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:uploadExecutionRun {
container = 'gudmaprbk/deriva1.4:1.0.0'
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:uploadQC {
container = 'gudmaprbk/deriva1.4:1.0.0'
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:uploadProcessedFile {
container = 'gudmaprbk/deriva1.4:1.0.0'
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:uploadOutputBag {
container = 'gudmaprbk/deriva1.4:1.0.0'
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:finalizeExecutionRun {
container = 'gudmaprbk/deriva1.4:1.0.0'
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:failPreExecutionRun {
container = 'gudmaprbk/deriva1.4:1.0.0'
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:failExecutionRun {
container = 'gudmaprbk/deriva1.4:1.0.0'
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:uploadQC_fail {
container = 'gudmaprbk/deriva1.4:1.0.0'
container = 'gudmaprbk/deriva1.4:1.0.1'
}
}
......
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