Merge pull request #4 from nf-core/dev

Release v1.0.0 -> v1.1.0

Author: sguizard

CHANGELOG.md

@@ -3,6 +3,30 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.1.0 - Black Crow [XX/07/2022]
+
+Improves computation time.
+Split `uLTRA pipeline` into two processes, `uLTRA index` and `uLTRA align`. `GTF` index is computed once and not `chunk` times.
+`uLTRA align` sort and convert `sam` output into `bam` files. Aligned reads are already sorted by `minimap2` module. Therefore, `samtools sort` module is not needed anymore and has been removed.
+The `bioperl` module objective was to deal with [spurious alignments produced by uLTRA if a malformed GTF is used](https://github.com/ksahlin/ultra/issues/11). Removing it will stop the pipeline in case of malformed `GTF`.
+Module resource requirements have been revised for four modules (`gstama/merge`, `isoseq3/refine`, `lima`, `ultra/align`) to reduce requested resources.
+AWS runs with shows better run time and CPU/RAM usage ([Results](docs/images/Isoseq_pipeline_v1.0.0_v1.1.0.png)).
+
+### `Added`
+
+- Add `uLTRA index` and `uLTRA align` to replace `uLTRA pipeline` [PR 1830](https://github.com/nf-core/modules/pull/1830)
+- Module resources adjustments: `gstama/merge`, `isoseq3/refine`, `lima`, `ultra/align` [PR1858](https://github.com/nf-core/modules/pull/1858), `gunzip`, `MultiQC`
+
+### `Fixed`
+
+### `Dependencies`
+
+### `Deprecated`
+
+- Remove `uLTRA pipeline`
+- Remove `samtools sort` module
+- Remove `bioperl` module
+
 ## v1.0.0 - Silver Swan [28/06/2022]
 
 Initial release of nf-core/isoseq, created with the [nf-core](https://nf-co.re/) template.

README.md

@@ -41,11 +41,10 @@ On release, automated continuous integration tests run the pipeline on a full-si
 4. Convert bam file into fasta file ([`BAMTOOLS CONVERT`](https://github.com/pezmaster31/bamtools))
 5. Select reads with a polyA tail and trim it ([`GSTAMA_POLYACLEANUP`](https://github.com/GenomeRIK/tama))
 6. uLTRA path: decompress FLNCs ([`GUNZIP`](https://www.gnu.org/software/gzip/))
-7. Map consensuses on the reference genome ([`MINIMAP2`](https://github.com/lh3/minimap2) or [`uLTRA`](https://github.com/ksahlin/ultra))
-8. uLTRA path remove spurious alignments ([`BIOPERL`](https://bioperl.org/))
-9. Sort sam file and convert bam ([`SAMTOOLS SORT`](http://www.htslib.org/doc/samtools-sort.html))
-10. Clean gene models ([`TAMA collapse`](https://github.com/GenomeRIK/tama))
-11. Merge annotations by sample ([`TAMA merge`](https://github.com/GenomeRIK/tama))
+7. uLTRA path: index `GTF` file for mapping ([`uLTRA`](https://github.com/ksahlin/ultra))
+8. Map consensuses on the reference genome ([`MINIMAP2`](https://github.com/lh3/minimap2) or [`uLTRA`](https://github.com/ksahlin/ultra))
+9. Clean gene models ([`TAMA collapse`](https://github.com/GenomeRIK/tama))
+10. Merge annotations by sample ([`TAMA merge`](https://github.com/GenomeRIK/tama))
 
 ## Quick Start
 
@@ -83,6 +82,7 @@ nf-core/isoseq was originally written by Sébastien Guizard.
 We thank the following people for their extensive assistance in the development of this pipeline:
 
 - Thanks to [Jose Espinosa-Carrasco](https://github.com/JoseEspinosa), [Daniel Schreyer](https://github.com/DSchreyer) and [Gisela Gabernet](https://github.com/ggabernet) for their reviews and contributions
+- [Kristoffer Sahlin](https://github.com/ksahlin) for `uLTRA` and the help he provided
 - [Richard Kuo](https://github.com/GenomeRIK) ([Wobble Genomics](https://www.wobblegenomics.com/)) for his valuable advices on isoseq analysis
 - The Workpackage 2 of [GENE-SWitCH Project](https://www.gene-switch.eu/) for their fruitful discussions and remarks
 - [Mick Watson](https://twitter.com/BioMickWatson) group for their support

conf/modules.config

@@ -81,38 +81,27 @@ process {
         ext.prefix = { "${meta.id}_tama" }
     }
 
-    withName: ULTRA_PIPELINE {
+    withName: ULTRA_INDEX {
         publishDir = [
-            path: { "${params.outdir}/06.2_ULTRA" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-        ext.args = "--isoseq --disable_infer"
-    }
-
-    withName: PERL_BIOPERL {
-        publishDir = [
-            path: { "${params.outdir}/06.3_PERL_BIOPERL" },
+            path: { "${params.outdir}/ULTRA_INDEX" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
-        ext.args = '-F\'\\t\' -nae \'print if ($F[5] !~ /N$/)\''
-        ext.prefix = { "${meta.id}_filtered.sam" }
     }
 
-    withName: SAMTOOLS_SORT {
+    withName: ULTRA_ALIGN {
         publishDir = [
-            path: { "${params.outdir}/07_SAMTOOLS_SORT" },
+            path: { "${params.outdir}/06.2_ULTRA" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
-        ext.prefix = { "${meta.id}_sorted" }
+        ext.args = "--isoseq"
     }
 
     if (params.capped == true) {
         withName: GSTAMA_COLLAPSE {
             publishDir = [
-                path: { "${params.outdir}/08_GSTAMA_COLLAPSE" },
+                path: { "${params.outdir}/07_GSTAMA_COLLAPSE" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
@@ -121,7 +110,7 @@ process {
     } else {
         withName: GSTAMA_COLLAPSE {
             publishDir = [
-                path: { "${params.outdir}/08_GSTAMA_COLLAPSE" },
+                path: { "${params.outdir}/07_GSTAMA_COLLAPSE" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
@@ -131,15 +120,15 @@ process {
 
     withName: GSTAMA_FILELIST {
         publishDir = [
-            path: { "${params.outdir}/09_GSTAMA_FILELIST" },
+            path: { "${params.outdir}/08_GSTAMA_FILELIST" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: GSTAMA_MERGE {
         publishDir = [
-            path: { "${params.outdir}/10_GSTAMA_MERGE" },
+            path: { "${params.outdir}/09_GSTAMA_MERGE" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]