diff --git a/CHANGELOG.md b/CHANGELOG.md index f2b29a63f..d2797457d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [PR #1376](https://github.com/nf-core/rnaseq/pull/1376) - Fix invalid named parameter syntax - [PR #1386](https://github.com/nf-core/rnaseq/pull/1386) - Bump pipeline version to 3.16.0dev - [PR #1388](https://github.com/nf-core/rnaseq/pull/1388) - Adding Kraken2/Bracken on unaligned reads as an additional quality control step to detect sample contamination +- [PR #1389](https://github.com/nf-core/rnaseq/pull/1389) - Update animated subway map ### Parameters diff --git a/docs/images/nf-core-rnaseq_metro_map_grey.png b/docs/images/nf-core-rnaseq_metro_map_grey.png index 1cb1cf32f..79b4e2afc 100644 Binary files a/docs/images/nf-core-rnaseq_metro_map_grey.png and b/docs/images/nf-core-rnaseq_metro_map_grey.png differ diff --git a/docs/images/nf-core-rnaseq_metro_map_grey.svg b/docs/images/nf-core-rnaseq_metro_map_grey.svg index c36c3e839..2de5cd2e3 100644 --- a/docs/images/nf-core-rnaseq_metro_map_grey.svg +++ b/docs/images/nf-core-rnaseq_metro_map_grey.svg @@ -7,7 +7,7 @@ viewBox="0 0 646.4851 269.92565" version="1.1" id="svg8" - inkscape:version="1.3.2 (091e20e, 2023-11-25)" + inkscape:version="1.3.2 (1:1.3.2+202311252150+091e20ef0f)" sodipodi:docname="nf-core-rnaseq_metro_map_grey.svg" inkscape:export-filename="nf-core-rnaseq_metro_map_grey.png" inkscape:export-xdpi="89" @@ -21,7 +21,12 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:cc="http://creativecommons.org/ns#" xmlns:dc="http://purl.org/dc/elements/1.1/">1catfastqSTAGE2. Genome alignment & quantification3. Pseudo-alignment & quantification1. Pre-processing4. Post-processingRSeQC(multiple modules)Kraken2/Bracken3SalmonKallistoMultiQCTSV54SAMtools(sort, index, stats)BEDtoolsgenomecov GermlineSarek  Exome GermlineSarek  Exome GermlineSarek  ExomeHTML GermlineSarek 1catfastqSTAGE2. Genome alignment & quantification3. Pseudo-alignment & quantification1. Pre-processing4. Post-processing35412 +  GermlineSarek  Exome GermlineSarek TSV Exome diff --git a/docs/images/nf-core-rnaseq_metro_map_grey_animated.svg b/docs/images/nf-core-rnaseq_metro_map_grey_animated.svg index 96ea8972a..8886dd962 100644 --- a/docs/images/nf-core-rnaseq_metro_map_grey_animated.svg +++ b/docs/images/nf-core-rnaseq_metro_map_grey_animated.svg @@ -21,7 +21,12 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:cc="http://creativecommons.org/ns#" xmlns:dc="http://purl.org/dc/elements/1.1/">5 + href="#hisat2_trimgalore" /> + href="#hisat2_fastp" /> + href="#hisat2_trimgalore" /> + href="#hisat2_fastp" /> + id="text74" + style="font-size:76.4916px;line-height:1;font-family:'DejaVu Sans Mono';-inkscape-font-specification:'DejaVu Sans Mono';white-space:pre;fill:#ffffff;stroke-width:15.1181;stroke-linecap:round;stroke-linejoin:round" + transform="matrix(0.09223963,0,0,0.09223963,199.99988,-1.0793955)" + aria-label="Kraken2/ Bracken">