From 647c95b2226f129d00e3a89a3cffc0e1c800dc32 Mon Sep 17 00:00:00 2001 From: James Ashmore Date: Sun, 21 Apr 2024 11:41:58 +0100 Subject: [PATCH 1/2] Fix incorrect assignment of cluster groups --- assets/multiqc_config.yml | 4 ++-- modules/local/suppa_clusterevents.nf | 2 +- modules/local/suppa_clustergroups.nf | 2 +- nextflow.config | 2 +- subworkflows/local/suppa.nf | 18 ++++++++++++++++++ 5 files changed, 23 insertions(+), 5 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 059da2f..2d69911 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/rnasplice + This report has been generated by the nf-core/rnasplice analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-rnasplice-methods-description": diff --git a/modules/local/suppa_clusterevents.nf b/modules/local/suppa_clusterevents.nf index b459812..6aa9bef 100644 --- a/modules/local/suppa_clusterevents.nf +++ b/modules/local/suppa_clusterevents.nf @@ -11,7 +11,7 @@ process CLUSTEREVENTS { input: tuple val(cond1), val(cond2), path(dpsi) tuple val(cond1), val(cond2), path(psivec) - val group_ranges // e.g. 1-3,4-6 + tuple val(cond1), val(cond2), val(group_ranges) // e.g. 1-3,4-6 val prefix val clusterevents_dpsithreshold // val params.clusterevents_dpsithreshold val clusterevents_eps // val params.clusterevents_eps diff --git a/modules/local/suppa_clustergroups.nf b/modules/local/suppa_clustergroups.nf index a556bdc..fe45ea8 100644 --- a/modules/local/suppa_clustergroups.nf +++ b/modules/local/suppa_clustergroups.nf @@ -11,7 +11,7 @@ process CLUSTERGROUPS { tuple val(cond1), val(cond2), path(psivec) output: - stdout + tuple val(cond1), val(cond2), stdout when: task.ext.when == null || task.ext.when diff --git a/nextflow.config b/nextflow.config index 2f63b75..800e272 100644 --- a/nextflow.config +++ b/nextflow.config @@ -356,7 +356,7 @@ manifest { description = """Alternative splicing analysis using RNA-seq.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.0.3' + version = '1.0.4' doi = '10.5281/zenodo.8424632' } diff --git a/subworkflows/local/suppa.nf b/subworkflows/local/suppa.nf index fe98a88..9483970 100644 --- a/subworkflows/local/suppa.nf +++ b/subworkflows/local/suppa.nf @@ -209,6 +209,15 @@ workflow SUPPA { ch_groups_ioe = CLUSTERGROUPS_IOE.out + // Join channels to ensure consistent order + + ch_clusterevents_ioe = ch_dpsi_local.join(ch_psivec_local, by: [0, 1]).join(ch_groups_ioe, by: [0, 1]) + + // Splitting the joined channel back into three separate channels + ch_dpsi_local = ch_clusterevents_ioe.map { it -> [it[0], it[1], it[2]] } + ch_psivec_local = ch_clusterevents_ioe.map { it -> [it[0], it[1], it[3]] } + ch_groups_ioe = ch_clusterevents_ioe.map { it -> [it[0], it[1], it[4]] } + // Run Clustering CLUSTEREVENTS_IOE( @@ -360,6 +369,15 @@ workflow SUPPA { ch_groups_ioi = CLUSTERGROUPS_IOI.out + // Join channels to ensure consistent order + + ch_clusterevents_ioi = ch_dpsi_isoform.join(ch_psivec_isoform, by: [0, 1]).join(ch_groups_ioi, by: [0, 1]) + + // Splitting the joined channel back into three separate channels + ch_dpsi_isoform = ch_clusterevents_ioi.map { it -> [it[0], it[1], it[2]] } + ch_psivec_isoform = ch_clusterevents_ioi.map { it -> [it[0], it[1], it[3]] } + ch_groups_ioi = ch_clusterevents_ioi.map { it -> [it[0], it[1], it[4]] } + // Run Clustering CLUSTEREVENTS_IOI( From e5ee51e497711b27fa6a9395c7b2809d13c66eda Mon Sep 17 00:00:00 2001 From: James Ashmore Date: Sun, 21 Apr 2024 11:57:42 +0100 Subject: [PATCH 2/2] Update CHANGELOG --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index de1cc28..6302447 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,10 @@ 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). +## v1.0.4 - 2024-04-21 + +- Fixed incorrect assignment of cluster groups (Issue #131). + ## v1.0.3 - 2024-02-23 - Improved TPM file splitting performance (Issue #120).