Merge pull request #739 from nf-core/dev

Patch release 2.3.4

Author: jfy133

.github/workflows/ci.yml

@@ -34,13 +34,13 @@ jobs:
 
       - name: Build new docker image
         if: env.MATCHED_FILES
-        run: docker build --no-cache . -t nfcore/eager:2.3.3
+        run: docker build --no-cache . -t nfcore/eager:2.3.4
 
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull nfcore/eager:dev
-          docker tag nfcore/eager:dev nfcore/eager:2.3.3
+          docker tag nfcore/eager:dev nfcore/eager:2.3.4
 
       - name: Install Nextflow
         env:

CHANGELOG.md

@@ -3,7 +3,28 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## v2.3.3 - 2021-01-06
+## v2.3.4 - 2021-05-05
+
+### `Added`
+
+- [#729](https://github.com/nf-core/eager/issues/729) Added Bowtie2 flag `--maxins` for PE mapping modern DNA mapping contexts
+
+### `Fixed`
+
+- Corrected explanation of the "--min_adap_overlap" parameter for AdapterRemoval in the docs
+- [#725](https://github.com/nf-core/eager/pull/725) `bwa_index` doc update
+- Re-adds gzip piping to AdapterRemovalFixPrefix to speed up process after reports of being very slow
+- Updated DamageProfiler citation from bioRxiv to publication
+
+### `Dependencies`
+
+- Removed pinning of `tbb` (upstream bug in bioconda fixed)
+- Bumped `pigz` to 2.6 to fix rare stall bug when compressing data after AdapterRemoval
+- Bumped Bowtie2 to 2.4.2 to fix issues with `tbb` version
+
+### `Deprecated`
+
+## v2.3.3 - 2021-04-08
 
 ### `Added`
 

Dockerfile

@@ -7,10 +7,10 @@ COPY environment.yml /
 RUN conda env create --quiet -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-eager-2.3.3/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.3.4/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-eager-2.3.3 > nf-core-eager-2.3.3.yml
+RUN conda env export --name nf-core-eager-2.3.4 > nf-core-eager-2.3.4.yml
 
 # Instruct R processes to use these empty files instead of clashing with a local version
 RUN touch .Rprofile

README.md

@@ -207,7 +207,7 @@ In addition, references of tools and data used in this pipeline are as follows:
 * **AdapterRemoval v2** Schubert, M., Lindgreen, S., & Orlando, L. (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 9, 88. [https://doi.org/10.1186/s13104-016-1900-2](https://doi.org/10.1186/s13104-016-1900-2). Download: [https://github.com/MikkelSchubert/adapterremoval](https://github.com/MikkelSchubert/adapterremoval)
 * **bwa** Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics , 25(14), 1754–1760. [https://doi.org/10.1093/bioinformatics/btp324](https://doi.org/10.1093/bioinformatics/btp324). Download: [http://bio-bwa.sourceforge.net/bwa.shtml](http://bio-bwa.sourceforge.net/bwa.shtml)
 * **SAMtools** Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., … 1000 Genome Project Data Processing Subgroup. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics , 25(16), 2078–2079. [https://doi.org/10.1093/bioinformatics/btp352](https://doi.org/10.1093/bioinformatics/btp352). Download: [http://www.htslib.org/](http://www.htslib.org/)
-* **DamageProfiler** Neukamm, J., Peltzer, A., & Nieselt, K. (2020). DamageProfiler: Fast damage pattern calculation for ancient DNA. In biorXiv (p. 2020.10.01.322206). [https://doi.org/10.1101/2020.10.01.322206](https://doi.org/10.1101/2020.10.01.322206). Download: [https://github.com/Integrative-Transcriptomics/DamageProfiler](https://github.com/Integrative-Transcriptomics/DamageProfiler)
+* **DamageProfiler** Neukamm, J., Peltzer, A., & Nieselt, K. (2020). DamageProfiler: Fast damage pattern calculation for ancient DNA. In Bioinformatics (btab190). [https://doi.org/10.1093/bioinformatics/btab190](https://doi.org/10.1093/bioinformatics/btab190). Download: [https://github.com/Integrative-Transcriptomics/DamageProfiler](https://github.com/Integrative-Transcriptomics/DamageProfiler)
 * **QualiMap** Okonechnikov, K., Conesa, A., & García-Alcalde, F. (2016). Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics , 32(2), 292–294. [https://doi.org/10.1093/bioinformatics/btv566](https://doi.org/10.1093/bioinformatics/btv566). Download: [http://qualimap.bioinfo.cipf.es/](http://qualimap.bioinfo.cipf.es/)
 * **preseq** Daley, T., & Smith, A. D. (2013). Predicting the molecular complexity of sequencing libraries. Nature Methods, 10(4), 325–327. [https://doi.org/10.1038/nmeth.2375](https://doi.org/10.1038/nmeth.2375). Download: [http://smithlabresearch.org/software/preseq/](http://smithlabresearch.org/software/preseq/)
 * **PMDTools** Skoglund, P., Northoff, B. H., Shunkov, M. V., Derevianko, A. P., Pääbo, S., Krause, J., & Jakobsson, M. (2014). Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. Proceedings of the National Academy of Sciences of the United States of America, 111(6), 2229–2234. [https://doi.org/10.1073/pnas.1318934111](https://doi.org/10.1073/pnas.1318934111). Download: [https://github.com/pontussk/PMDtools](https://github.com/pontussk/PMDtools)