Merge pull request #801 from drpatelh/sync

Update CHANGELOG after merging template updates

Author: drpatelh

.github/workflows/awsfulltest.yml

@@ -30,6 +30,3 @@ jobs:
               "aligner": "${{ matrix.aligner }}"
             }
           profiles: test_full,aws_tower
-          nextflow_config: |
-            process.errorStrategy = 'retry'
-            process.maxRetries = 3

.github/workflows/awstest.yml

@@ -23,6 +23,3 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnaseq/results-test-${{ github.sha }}"
             }
           profiles: test,aws_tower
-          nextflow_config: |
-            process.errorStrategy = 'retry'
-            process.maxRetries = 3

.github/workflows/ci.yml

@@ -144,4 +144,4 @@ jobs:
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results
 
-#
+#

.nf-core.yml

@@ -4,10 +4,6 @@ lint:
     - assets/email_template.html
     - assets/email_template.txt
     - lib/NfcoreTemplate.groovy
-    - .github/PULL_REQUEST_TEMPLATE.md
-    - .github/workflows/branch.yml
-    - .github/workflows/linting_comment.yml
-    - .github/workflows/linting.yml
 update:
   nf-core/modules:
     rseqc/bamstat: "e745e167c1020928ef20ea1397b6b4d230681b4d"

.prettierignore

@@ -0,0 +1,8 @@
+.nextflow*
+work/
+data/
+results/
+.DS_Store
+testing/
+testing*
+*.pyc

CHANGELOG.md

@@ -10,90 +10,113 @@
 
 ## Pipeline tools
 
-* [BBMap](https://sourceforge.net/projects/bbmap/)
+- [BBMap](https://sourceforge.net/projects/bbmap/)
 
-* [BEDTools](https://pubmed.ncbi.nlm.nih.gov/20110278/)
-    > Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824.
+- [BEDTools](https://pubmed.ncbi.nlm.nih.gov/20110278/)
 
-* [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+  > Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824.
 
-* [featureCounts](https://pubmed.ncbi.nlm.nih.gov/24227677/)
-    > Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014 Apr 1;30(7):923-30. doi: 10.1093/bioinformatics/btt656. Epub 2013 Nov 13. PubMed PMID: 24227677.
+- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
-* [GffRead](https://pubmed.ncbi.nlm.nih.gov/32489650/)
-    > Pertea G, Pertea M. GFF Utilities: GffRead and GffCompare. F1000Res. 2020 Apr 28;9:ISCB Comm J-304. doi: 10.12688/f1000research.23297.2. eCollection 2020. PubMed PMID: 32489650; PubMed Central PMCID: PMC7222033.
+- [featureCounts](https://pubmed.ncbi.nlm.nih.gov/24227677/)
 
-* [HISAT2](https://pubmed.ncbi.nlm.nih.gov/31375807/)
-    > Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4. Epub 2019 Aug 2. PubMed PMID: 31375807.
+  > Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014 Apr 1;30(7):923-30. doi: 10.1093/bioinformatics/btt656. Epub 2013 Nov 13. PubMed PMID: 24227677.
 
-* [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
-    > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
+- [GffRead](https://pubmed.ncbi.nlm.nih.gov/32489650/)
 
-* [picard-tools](http://broadinstitute.github.io/picard)
+  > Pertea G, Pertea M. GFF Utilities: GffRead and GffCompare. F1000Res. 2020 Apr 28;9:ISCB Comm J-304. doi: 10.12688/f1000research.23297.2. eCollection 2020. PubMed PMID: 32489650; PubMed Central PMCID: PMC7222033.
 
-* [preseq](https://pubmed.ncbi.nlm.nih.gov/23435259/)
-    > Daley T, Smith AD. Predicting the molecular complexity of sequencing libraries. Nat Methods. 2013 Apr;10(4):325-7. doi: 10.1038/nmeth.2375. Epub 2013 Feb 24. PubMed PMID: 23435259; PubMed Central PMCID: PMC3612374.
+- [HISAT2](https://pubmed.ncbi.nlm.nih.gov/31375807/)
 
-* [Qualimap 2](https://pubmed.ncbi.nlm.nih.gov/26428292/)
-    > Okonechnikov K, Conesa A, García-Alcalde F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data Bioinformatics. 2016 Jan 15;32(2):292-4. doi: 10.1093/bioinformatics/btv566. Epub 2015 Oct 1. PubMed PMID: 26428292; PubMed Central PMCID: PMC4708105.
+  > Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4. Epub 2019 Aug 2. PubMed PMID: 31375807.
 
-* [RSEM](https://pubmed.ncbi.nlm.nih.gov/21816040/)
-    > Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome BMC Bioinformatics. 2011 Aug 4;12:323. doi: 10.1186/1471-2105-12-323. PubMed PMID: 21816040; PubMed Central PMCID: PMC3163565.
+- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
-* [RSeQC](https://pubmed.ncbi.nlm.nih.gov/22743226/)
-    > Wang L, Wang S, Li W. RSeQC: quality control of RNA-seq experiments Bioinformatics. 2012 Aug 15;28(16):2184-5. doi: 10.1093/bioinformatics/bts356. Epub 2012 Jun 27. PubMed PMID: 22743226.
+  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
-* [Salmon](https://pubmed.ncbi.nlm.nih.gov/28263959/)
-    > Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression Nat Methods. 2017 Apr;14(4):417-419. doi: 10.1038/nmeth.4197. Epub 2017 Mar 6. PubMed PMID: 28263959; PubMed Central PMCID: PMC5600148.
+- [picard-tools](http://broadinstitute.github.io/picard)
 
-* [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/)
-    > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.
+- [preseq](https://pubmed.ncbi.nlm.nih.gov/23435259/)
 
-* [SortMeRNA](https://pubmed.ncbi.nlm.nih.gov/23071270/)
-    > Kopylova E, Noé L, Touzet H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data Bioinformatics. 2012 Dec 15;28(24):3211-7. doi: 10.1093/bioinformatics/bts611. Epub 2012 Oct 15. PubMed PMID: 23071270.
+  > Daley T, Smith AD. Predicting the molecular complexity of sequencing libraries. Nat Methods. 2013 Apr;10(4):325-7. doi: 10.1038/nmeth.2375. Epub 2013 Feb 24. PubMed PMID: 23435259; PubMed Central PMCID: PMC3612374.
 
-* [STAR](https://pubmed.ncbi.nlm.nih.gov/23104886/)
-    > Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905.
+- [Qualimap 2](https://pubmed.ncbi.nlm.nih.gov/26428292/)
 
-* [StringTie2](https://pubmed.ncbi.nlm.nih.gov/31842956/)
-    > Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly from long-read RNA-seq alignments with StringTie2 Genome Biol. 2019 Dec 16;20(1):278. doi: 10.1186/s13059-019-1910-1. PubMed PMID: 31842956; PubMed Central PMCID: PMC6912988.
+  > Okonechnikov K, Conesa A, García-Alcalde F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data Bioinformatics. 2016 Jan 15;32(2):292-4. doi: 10.1093/bioinformatics/btv566. Epub 2015 Oct 1. PubMed PMID: 26428292; PubMed Central PMCID: PMC4708105.
 
-* [Trim Galore!](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
+- [RSEM](https://pubmed.ncbi.nlm.nih.gov/21816040/)
 
-* [UMI-tools](https://pubmed.ncbi.nlm.nih.gov/28100584/)
-    > Smith T, Heger A, Sudbery I. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy Genome Res. 2017 Mar;27(3):491-499. doi: 10.1101/gr.209601.116. Epub 2017 Jan 18. PubMed PMID: 28100584; PubMed Central PMCID: PMC5340976.
+  > Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome BMC Bioinformatics. 2011 Aug 4;12:323. doi: 10.1186/1471-2105-12-323. PubMed PMID: 21816040; PubMed Central PMCID: PMC3163565.
 
-* [UCSC tools](https://pubmed.ncbi.nlm.nih.gov/20639541/)
-    > Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010 Sep 1;26(17):2204-7. doi: 10.1093/bioinformatics/btq351. Epub 2010 Jul 17. PubMed PMID: 20639541; PubMed Central PMCID: PMC2922891.
+- [RSeQC](https://pubmed.ncbi.nlm.nih.gov/22743226/)
+
+  > Wang L, Wang S, Li W. RSeQC: quality control of RNA-seq experiments Bioinformatics. 2012 Aug 15;28(16):2184-5. doi: 10.1093/bioinformatics/bts356. Epub 2012 Jun 27. PubMed PMID: 22743226.
+
+- [Salmon](https://pubmed.ncbi.nlm.nih.gov/28263959/)
+
+  > Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression Nat Methods. 2017 Apr;14(4):417-419. doi: 10.1038/nmeth.4197. Epub 2017 Mar 6. PubMed PMID: 28263959; PubMed Central PMCID: PMC5600148.
+
+- [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/)
+
+  > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.
+
+- [SortMeRNA](https://pubmed.ncbi.nlm.nih.gov/23071270/)
+
+  > Kopylova E, Noé L, Touzet H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data Bioinformatics. 2012 Dec 15;28(24):3211-7. doi: 10.1093/bioinformatics/bts611. Epub 2012 Oct 15. PubMed PMID: 23071270.
+
+- [STAR](https://pubmed.ncbi.nlm.nih.gov/23104886/)
+
+  > Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905.
+
+- [StringTie2](https://pubmed.ncbi.nlm.nih.gov/31842956/)
+
+  > Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly from long-read RNA-seq alignments with StringTie2 Genome Biol. 2019 Dec 16;20(1):278. doi: 10.1186/s13059-019-1910-1. PubMed PMID: 31842956; PubMed Central PMCID: PMC6912988.
+
+- [Trim Galore!](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
+
+- [UMI-tools](https://pubmed.ncbi.nlm.nih.gov/28100584/)
+
+  > Smith T, Heger A, Sudbery I. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy Genome Res. 2017 Mar;27(3):491-499. doi: 10.1101/gr.209601.116. Epub 2017 Jan 18. PubMed PMID: 28100584; PubMed Central PMCID: PMC5340976.
+
+- [UCSC tools](https://pubmed.ncbi.nlm.nih.gov/20639541/)
+  > Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010 Sep 1;26(17):2204-7. doi: 10.1093/bioinformatics/btq351. Epub 2010 Jul 17. PubMed PMID: 20639541; PubMed Central PMCID: PMC2922891.
 
 ## R packages
 
-* [R](https://www.R-project.org/)
-    > R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
+- [R](https://www.R-project.org/)
+
+  > R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
+
+- [DESeq2](https://pubmed.ncbi.nlm.nih.gov/25516281/)
+
+  > Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. PubMed PMID: 25516281; PubMed Central PMCID: PMC4302049.
+
+- [dupRadar](https://pubmed.ncbi.nlm.nih.gov/27769170/)
+
+  > Sayols S, Scherzinger D, Klein H. dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data BMC Bioinformatics. 2016 Oct 21;17(1):428. doi: 10.1186/s12859-016-1276-2. PubMed PMID: 27769170; PubMed Central PMCID: PMC5073875.
+
+- [ggplot2](https://cran.r-project.org/web/packages/ggplot2/index.html)
+
+  > H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.
+
+- [optparse](https://CRAN.R-project.org/package=optparse)
 
-* [DESeq2](https://pubmed.ncbi.nlm.nih.gov/25516281/)
-    > Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. PubMed PMID: 25516281; PubMed Central PMCID: PMC4302049.
+  > Trevor L Davis (2018). optparse: Command Line Option Parser.
 
-* [dupRadar](https://pubmed.ncbi.nlm.nih.gov/27769170/)
-    > Sayols S, Scherzinger D, Klein H. dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data BMC Bioinformatics. 2016 Oct 21;17(1):428. doi: 10.1186/s12859-016-1276-2. PubMed PMID: 27769170; PubMed Central PMCID: PMC5073875.
+- [pheatmap](https://CRAN.R-project.org/package=pheatmap)
 
-* [ggplot2](https://cran.r-project.org/web/packages/ggplot2/index.html)
-    > H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.
+  > Raivo Kolde (2018). pheatmap: Pretty Heatmaps.
 
-* [optparse](https://CRAN.R-project.org/package=optparse)
-    > Trevor L Davis (2018). optparse: Command Line Option Parser.
+- [RColorBrewer](https://CRAN.R-project.org/package=RColorBrewer)
 
-* [pheatmap](https://CRAN.R-project.org/package=pheatmap)
-    > Raivo Kolde (2018). pheatmap: Pretty Heatmaps.
+  > Erich Neuwirth (2014). RColorBrewer: ColorBrewer Palettes.
 
-* [RColorBrewer](https://CRAN.R-project.org/package=RColorBrewer)
-    > Erich Neuwirth (2014). RColorBrewer: ColorBrewer Palettes.
+- [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html)
 
-* [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html)
-    > Morgan M, Obenchain V, Hester J and Pagès H (2020). SummarizedExperiment: SummarizedExperiment container.
+  > Morgan M, Obenchain V, Hester J and Pagès H (2020). SummarizedExperiment: SummarizedExperiment container.
 
-* [Tximeta](https://pubmed.ncbi.nlm.nih.gov/32097405/)
-    > Love MI, Soneson C, Hickey PF, Johnson LK, Pierce NT, Shepherd L, Morgan M, Patro R. Tximeta: Reference sequence checksums for provenance identification in RNA-seq PLoS Comput Biol. 2020 Feb 25;16(2):e1007664. doi: 10.1371/journal.pcbi.1007664. eCollection 2020 Feb. PubMed PMID: 32097405; PubMed Central PMCID: PMC7059966.
+- [Tximeta](https://pubmed.ncbi.nlm.nih.gov/32097405/)
+  > Love MI, Soneson C, Hickey PF, Johnson LK, Pierce NT, Shepherd L, Morgan M, Patro R. Tximeta: Reference sequence checksums for provenance identification in RNA-seq PLoS Comput Biol. 2020 Feb 25;16(2):e1007664. doi: 10.1371/journal.pcbi.1007664. eCollection 2020 Feb. PubMed PMID: 32097405; PubMed Central PMCID: PMC7059966.
 
 ## Software packaging/containerisation tools