nf-core · drpatelh · Sep 29, 2022 · Sep 25, 2022 · Sep 25, 2022 · Sep 25, 2022
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+- [[#746](https://github.com/nf-core/rnaseq/issues/746)] - Add `tin.py` output to MultiQC report
+- [[#841](https://github.com/nf-core/rnaseq/issues/841)] - Turn `--deseq2_vst` on by default
+- [[#857](https://github.com/nf-core/rnaseq/issues/857)] - Missing parameter required by StringTie if using STAR as aligner
+- [[#862](https://github.com/nf-core/rnaseq/issues/862)] - Filter samples that have no reads after trimming
 - Expose additional arguments to UMI-tools as pipeline params: `--umitools_bc_pattern2` is required if the UMI is located on read 2. `--umitools_umi_separator` will often be needed in conjunction with `--skip_umi_extract` as most other tools such as Illumina's `BCL Convert` use a colon instead of an underscore to separate the UMIs. The `--umitools_grouping_method` allows to fine-tune handling of similar but non-identical UMIs.
 - Updated pipeline template to [nf-core/tools 2.5.1](https://github.com/nf-core/tools/releases/tag/2.5.1)
 
@@ -18,6 +22,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 |               | `--umitools_umi_separator`   |
 |               | `--umitools_grouping_method` |
 
+### Software dependencies
+
+Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `multiqc`  | 1.11        | 1.13        |
+| `picard`   | 2.26.10     | 2.27.4      |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+> **NB:** Dependency has been **added** if just the new version information is present.
+> **NB:** Dependency has been **removed** if version information isn't present.
+
 ## [[3.8.1](https://github.com/nf-core/rnaseq/releases/tag/3.8.1)] - 2022-05-27
 
 - [[#834](https://github.com/nf-core/rnaseq/issues/834)] - `nf-core download` fails with version 3.8 of the pipeline

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -104,7 +104,7 @@ sp:
   rseqc/infer_experiment:
     fn: "*.infer_experiment.txt"
   rseqc/tin:
-    fn: "*.tin.txt"
+    fn: "*.summary.txt"
 
   picard/markdups:
     fn: "*.MarkDuplicates.metrics.txt"

diff --git a/conf/modules.config b/conf/modules.config
@@ -294,6 +294,7 @@ if (params.remove_ribo_rna) {
 if (!params.skip_alignment) {
     process {
         withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
+            ext.prefix = { "${meta.id}.sorted.bam" }
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}/samtools_stats" },
                 mode: params.publish_dir_mode,
@@ -333,7 +334,7 @@ if (!params.skip_alignment) {
     if (!params.skip_markduplicates) {
         process {
             withName: '.*:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES' {
-                ext.args   = 'ASSUME_SORTED=true REMOVE_DUPLICATES=false VALIDATION_STRINGENCY=LENIENT TMP_DIR=tmp'
+                ext.args   = '--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp'
                 ext.prefix = { "${meta.id}.markdup.sorted" }
                 publishDir = [
                     [
@@ -360,6 +361,7 @@ if (!params.skip_alignment) {
             }
 
             withName: '.*:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*' {
+                ext.prefix = { "${meta.id}.markdup.sorted.bam" }
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/samtools_stats" },
                     mode: params.publish_dir_mode,
@@ -413,6 +415,7 @@ if (!params.skip_alignment) {
             }
 
             withName: '.*:DEDUP_UMI_UMITOOLS_GENOME:BAM_STATS_SAMTOOLS:.*' {
+                ext.prefix = { "${meta.id}.umi_dedup.sorted.bam" }
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/samtools_stats" },
                     mode: params.publish_dir_mode,
@@ -513,6 +516,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                 '--alignSJDBoverhangMin 1',
                 '--outSAMattributes NH HI AS NM MD',
                 '--quantTranscriptomeBan Singleend',
+                '--outSAMstrandField intronMotif',
                 params.save_unaligned ? '--outReadsUnmapped Fastx' : ''
             ].join(' ').trim()
             publishDir = [
@@ -605,6 +609,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
             }
 
             withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
+                ext.prefix = { "${meta.id}.transcriptome.sorted.bam" }
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}" },
                     enabled: false
@@ -633,6 +638,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
             }
 
             withName: '.*:DEDUP_UMI_UMITOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:.*' {
+                ext.prefix = { "${meta.id}.umi_dedup.transcriptome.sorted.bam" }
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/samtools_stats" },
                     mode: params.publish_dir_mode,

diff --git a/docs/output.md b/docs/output.md
@@ -617,7 +617,7 @@ The [Preseq](http://smithlabresearch.org/software/preseq/) package is aimed at p
 
 The script included in the pipeline uses DESeq2 to normalise read counts across all of the provided samples in order to create a PCA plot and a clustered heatmap showing pairwise Euclidean distances between the samples in the experiment. These help to show the similarity between groups of samples and can reveal batch effects and other potential issues with the experiment.
 
-For larger experiments, it may be recommended to use the `vst` transformation instead of the default `rlog` option. You can do this by providing the `--deseq2_vst` parameter to the pipeline. See [DESeq2 docs](http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#data-transformations-and-visualization) for a more detailed explanation.
+By default, the pipeline uses the `vst` transformation which is more suited to larger experiments. You can set the parameter `--deseq2_vst false` if you wish to use the DESeq2 native `rlog` option. See [DESeq2 docs](http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#data-transformations-and-visualization) for a more detailed explanation.
 
 The PCA plots are generated based alternately on the top five hundred most variable genes, or all genes. The former is the conventional approach that is more likely to pick up strong effects (ie the biological signal) and the latter, when different, is picking up a weaker but consistent effect that is synchronised across many transcripts. We project both of these onto the first two PCs (shown in the top row of the figure below), which is the best two dimensional representation of the variation between samples.
 

diff --git a/modules.json b/modules.json
@@ -7,15 +7,15 @@
             "modules": {
                 "bbmap/bbsplit": {
                     "branch": "master",
-                    "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                    "git_sha": "848ee9a215d02d80be033bfa60881700f2bd914c"
                 },
                 "cat/fastq": {
                     "branch": "master",
-                    "git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
+                    "git_sha": "e9bc33485e420b51cfbed3cf63ac7463cd5739d3"
                 },
                 "custom/dumpsoftwareversions": {
                     "branch": "master",
-                    "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                    "git_sha": "82501fe6d0d12614db67751d30af98d16e63dc59"
                 },
                 "custom/getchromsizes": {
                     "branch": "master",
@@ -31,31 +31,31 @@
                 },
                 "gunzip": {
                     "branch": "master",
-                    "git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
+                    "git_sha": "90aef30f432332bdf0ce9f4b9004aa5d5c4960bb"
                 },
                 "hisat2/align": {
                     "branch": "master",
-                    "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
+                    "git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
                 },
                 "hisat2/build": {
                     "branch": "master",
-                    "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                    "git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
                 },
                 "hisat2/extractsplicesites": {
                     "branch": "master",
-                    "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                    "git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
                 },
                 "picard/markduplicates": {
                     "branch": "master",
-                    "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"
+                    "git_sha": "682f789f93070bd047868300dd018faf3d434e7c"
                 },
                 "preseq/lcextrap": {
                     "branch": "master",
-                    "git_sha": "7111e571cc5b6069de4673cd6165af680f17b4d7"
+                    "git_sha": "90aef30f432332bdf0ce9f4b9004aa5d5c4960bb"
                 },
                 "qualimap/rnaseq": {
                     "branch": "master",
-                    "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                    "git_sha": "82501fe6d0d12614db67751d30af98d16e63dc59"
                 },
                 "rsem/calculateexpression": {
                     "branch": "master",
@@ -107,67 +107,67 @@
                 },
                 "samtools/flagstat": {
                     "branch": "master",
-                    "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
+                    "git_sha": "bbb99cb8d679555cc01c98766de7869f83283545"
                 },
                 "samtools/idxstats": {
                     "branch": "master",
-                    "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
+                    "git_sha": "f0a86eaf5bf6ca73c5571193edd00c25bfa308f5"
                 },
                 "samtools/index": {
                     "branch": "master",
                     "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
                 },
                 "samtools/sort": {
                     "branch": "master",
-                    "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
+                    "git_sha": "d5d785b3d8b422cda9c6d84a23f629a8e9ff8cd8"
                 },
                 "samtools/stats": {
                     "branch": "master",
-                    "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
+                    "git_sha": "f4eab7945952dc4934224309701a49913ea05ae6"
                 },
                 "sortmerna": {
                     "branch": "master",
                     "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
                 },
                 "star/align": {
                     "branch": "master",
-                    "git_sha": "fb6c7bca3d55c19a793372513395e3a567bdd7ba"
+                    "git_sha": "cd22a76c78b09f7837a5a75642774a4bf48c92ba"
                 },
                 "star/genomegenerate": {
                     "branch": "master",
-                    "git_sha": "fb6c7bca3d55c19a793372513395e3a567bdd7ba"
+                    "git_sha": "cd22a76c78b09f7837a5a75642774a4bf48c92ba"
                 },
                 "stringtie/stringtie": {
                     "branch": "master",
-                    "git_sha": "6d88f2da8cc5d586456e801b535cc4213e0fa2f7"
+                    "git_sha": "47cc7a77bfa10c0aa6e6c393d09e895a85d1583e"
                 },
                 "subread/featurecounts": {
                     "branch": "master",
                     "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
                 },
                 "trimgalore": {
                     "branch": "master",
-                    "git_sha": "85ec13ff1fc2196c5a507ea497de468101baabed"
+                    "git_sha": "bfbdc4f79bb26bc698d30b74abd081db8af77f4d"
                 },
                 "ucsc/bedclip": {
                     "branch": "master",
-                    "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                    "git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
                 },
                 "ucsc/bedgraphtobigwig": {
                     "branch": "master",
-                    "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+                    "git_sha": "90aef30f432332bdf0ce9f4b9004aa5d5c4960bb"
                 },
                 "umitools/dedup": {
                     "branch": "master",
-                    "git_sha": "84f02a08a5d6d881cb18c31fb15faca4e735a1f2"
+                    "git_sha": "9d489648a7425fa18d8bed18935442c104d8733c"
                 },
                 "umitools/extract": {
                     "branch": "master",
                     "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
                 },
                 "untar": {
                     "branch": "master",
-                    "git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
+                    "git_sha": "b63b9f752dc8e43fc70b0491aad5e0a270ab0e10"
                 }
             }
         }

diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf
@@ -1,10 +1,10 @@
 process MULTIQC {
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::multiqc=1.11" : null)
+    conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
 
     input:
     path multiqc_config

diff --git a/modules/nf-core/modules/bbmap/bbsplit/meta.yml b/modules/nf-core/modules/bbmap/bbsplit/meta.yml
diff --git a/modules/nf-core/modules/cat/fastq/main.nf b/modules/nf-core/modules/cat/fastq/main.nf
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
diff --git a/modules/nf-core/modules/gunzip/main.nf b/modules/nf-core/modules/gunzip/main.nf