What’s Changed

• Move read.table out of loop by @jma1991 in #121
• Stop R converting sample names with ’-’ in string by @jma1991 in #124
• Patch fix v1.0.3 by @jma1991 in #125

Full Changelog: 1.0.2…1.0.3

What’s Changed

• Specify pScreenAdjusted argument depending on analysis method by @jma1991 in #113
• Add missing example contrastsheet by @jma1991 in #114
• Important! Template update for nf-core/tools v2.11.1 by @nf-core-bot in #110
• Patch fix v1.0.2 by @jma1991 in #115
• Release of patch fix v1.0.2 by @jma1991 in #116

Full Changelog: 1.0.1…1.0.2

What’s Changed

• add zenodo doi by @maxulysse in #96
• bump version by @jma1991 in #95
• cast command args to numeric by @jma1991 in #100
• Revert “cast command args to numeric” by @jma1991 in #101
• patch run drimseq filter by @jma1991 in #102
• Patch v1.0.1 by @jma1991 in #103

New Contributors

• @maxulysse made their first contribution in #96

Full Changelog: 1.0.0…1.0.1

What’s Changed

• Sl 29 implement featurecount module in #1
• Sl 35 rmats single condition by @bensouthgate in #2
• SL-33 implement edge deu module in #3
• SL-77 Add .github files in #4
• SL-78 update nf-core module structure imports in #5
• SL-70 Add strandedness,condition and validation code in #6
• SL-82 add groovy functions and include valid_params in #7
• SL-84 parametize gff type / add process_single tag in #8
• SL-86 refactor ch_samplesheet in #9
• SL-93 refactor rmarts input checks in #10
• SL-95 format bin python files in #11
• Sl 96 refactor aligner conditional behaviour in #12
• Sl 102 add condition check for rmats to groovy script in #13
• SL-101 add suppa parameter check in #14
• SL-107 typo correction in dex seq by @asmaali98 in #17
• SL-98 add rmats mulled container, resolve dexseq bug by @asmaali98 in #15
• SL-105 add getchromsizes to modules conf in #18
• SL-108 add single prep to withname pattern in #19
• Sl 64 write GitHub documentation by @bensouthgate in #20
• SL-106 check denominator specified correctly in #21
• SL-112 add warning for user in #22
• SL-104 fix withname pattern in #23
• SL-98 rmats read length correction by @asmaali98 in #24
• SL-118 respec modules conf in #25
• SL-119 add gtf_gene_filter to modules.config in #26
• SL-117 fix featurecounts spec in #27
• Sl 64 write GitHub documentation by @bensouthgate in #28
• Use script with echo + sed instead of exec with task.WorkDir for rMATS create_bamlist by @olgabot in #29
• SL-17 Include star_salmon_quant rule in modules.config by @claire-prince in #30
• SL-21 Include enable.conda in configuration by @claire-prince in #32
• SL-18 Update SAMTOOLS_INDEX publishDir pattern by @claire-prince in #34
• SL-13 Add param to turn off DEXSeq.gff output save by @claire-prince in #31
• Merging template updates by @bensouthgate in #37
• Important! Template update for nf-core/tools v2.7.2 by @nf-core-bot in #36
• remove enable_conda param by @jma1991 in #38
• fix samplesheet location by @jma1991 in #40
• fix duplicate exons and star segfault by @jma1991 in #41
• Fix module tests by @jma1991 in #42
• fixed some pipeline and module tests by @jma1991 in #43
• update singularity and docker containers by @jma1991 in #45
• add basic tower.yml file by @jma1991 in #46
• remove default values specified as None by @jma1991 in #47
• Test full by @jma1991 in #48
• update process capacity by @jma1991 in #49
• Bam and visualisation by @jma1991 in #50
• v1 of contrasts by @jma1991 in #53
• Merging template updates by @jma1991 in #54
• Important! Template update for nf-core/tools v2.8 by @nf-core-bot in #51
• fix lint tests v1 by @jma1991 in #55
• release steps by @jma1991 in #56
• prettier CHANGELOG by @jma1991 in #59
• Fixed params.gencode in prepare_genome - issue #60 by @valentinoruggieri in #61
• Revert “Fixed params.gencode in prepare_genome - issue #60” by @jma1991 in #62
• remove sniffer by @jma1991 in #64
• Fixed gencode issues by @valentinoruggieri in #65
• Revert “Fixed gencode issues” by @jma1991 in #66
• resolve gencode fix by @jma1991 in #67
• initial pass of fixes by @jma1991 in #68
• V1.0.0 release fixes by @jma1991 in #77
• Merging template updates by @jma1991 in #79
• Important! Template update for nf-core/tools v2.9 by @nf-core-bot in #73
• Fixes MISO scratch/launch directory and gffread issue by @jma1991 in #80
• keep contrasts as array when only one level by @jma1991 in #82
• suppa fix attempt 1 by @jma1991 in #86
• replace across with combine to mimic SQL join by @jma1991 in #87
• refactor rmats contrasts by @jma1991 in #88
• Potential fix for MISO index issue by @jma1991 in #91
• Important! Template update for nf-core/tools v2.10 by @nf-core-bot in #92
• pre-release fixes by @jma1991 in #94
• 1.0.0 release of nf-core/rnasplice pipeline by @jma1991 in #57

New Contributors

• @bensouthgate made their first contribution in #2
• @asmaali98 made their first contribution in #17
• @olgabot made their first contribution in #29
• @claire-prince made their first contribution in #30
• @nf-core-bot made their first contribution in #36
• @jma1991 made their first contribution in #38
• @valentinoruggieri made their first contribution in #61

Full Changelog: https://github.com/nf-core/rnasplice/commits/1.0.0