diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 141fc56791d1cea908250ece29e2b32dfe6a8355..1ba7c6df4d16a875b093c7322b4da1078a174bce 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -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
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 57bc30dfed523968bfa2fd0d078f10f25b5a6be9..d69f5809cbee8d9ecc3723df9b497571310c2403 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -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)
diff --git a/docs/software_references_mqc.yaml b/docs/software_references_mqc.yaml
index ac14c454cb40ac795d984c5b6c6a5970c56bd007..4d2164ac1da4196d4bb29b9add8bc839ef7eaec9 100644
--- a/docs/software_references_mqc.yaml
+++ b/docs/software_references_mqc.yaml
@@ -25,49 +25,49 @@
<ul>
<li>D'Arcy, M., Chard, K., Foster, I., Kesselman, C., Madduri, R., Saint, N., & 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>RamÃrez, 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>
diff --git a/docs/software_versions_mqc.yaml b/docs/software_versions_mqc.yaml
index 61c00f4b803d5da66cd19b930a1a15f74fa521ea..06585acbc9964a76d4ba1dff62a4d4464b73bd8e 100644
--- a/docs/software_versions_mqc.yaml
+++ b/docs/software_versions_mqc.yaml
@@ -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>
diff --git a/nextflow.config b/nextflow.config
index 7e046c710b26b487578556e4f77bba3708d48258..7f33391da6a455ba53664c35309c84b27b04d883 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -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'
}
}