nf-core/sarek issues and pull requests

#1180 - Update modules

Pull Request - State: closed - Opened by asp8200 11 months ago - 2 comments

#1179 - Unhide params trim_fastq, umi_read_structure, and aligner.

Pull Request - State: closed - Opened by robsyme 11 months ago - 3 comments

#1178 - Updating VEP to v110

Pull Request - State: closed - Opened by asp8200 11 months ago - 2 comments

#1177 - Status inference update

Pull Request - State: closed - Opened by FriederikeHanssen 11 months ago - 4 comments
Labels: Ready for Review

#1176 - Add Ascat tumor-only & targeted mode

Issue - State: open - Opened by FriederikeHanssen 11 months ago
Labels: enhancement

#1175 - nf-validation plugin: Status inference does not work

Issue - State: closed - Opened by FriederikeHanssen 11 months ago
Labels: bug, PR opened

#1174 - Updating multiqc to v1.15

Pull Request - State: closed - Opened by asp8200 11 months ago - 1 comment

#1173 - Fix GenomicsDB bug with mismatched intervals, remove duplicated variants from VQSR vcfs, add VQSR CI test

Pull Request - State: closed - Opened by FriederikeHanssen 11 months ago - 8 comments
Labels: Ready for Review, samplesheet

#1172 - Gvcf are published also when all intervals are processed at once

Pull Request - State: closed - Opened by FriederikeHanssen 11 months ago - 4 comments

#1171 - fix getpileupsummary should not run if no germline resource is provided

Pull Request - State: closed - Opened by FriederikeHanssen 11 months ago - 4 comments
Labels: testing

#1170 - Request to un-hide common parameters

Issue - State: closed - Opened by robsyme 11 months ago - 1 comment
Labels: enhancement, PR opened

#1169 - Updating sentieon-modules

Pull Request - State: closed - Opened by asp8200 11 months ago - 1 comment

#1168 - Unsucessful, at the `MergeVcfs` step when using `--joint_germline true`

Issue - State: open - Opened by MahShaaban 11 months ago - 4 comments
Labels: bug, moreinfo

#1167 - Sarek stops at MULTIQC step.

Issue - State: closed - Opened by portbo 11 months ago - 4 comments
Labels: bug

#1166 - note on '--tools' in Quickstart

Pull Request - State: closed - Opened by ATpoint 11 months ago - 6 comments

#1165 - sarek in slurm : issue

Issue - State: closed - Opened by ChitrArpita 11 months ago - 15 comments

#1164 - Moving error-handling to script section of sentieon-processes

Pull Request - State: closed - Opened by asp8200 11 months ago - 2 comments

#1163 - Correcting location of output folder for joint variant calling with h…

Pull Request - State: closed - Opened by asp8200 11 months ago - 2 comments

#1162 - Allow on restart to not convert the bam files to cram

Issue - State: open - Opened by YussAb 12 months ago
Labels: enhancement

#1161 - Nucleotides per second default to high

Issue - State: open - Opened by saulpierotti 12 months ago - 1 comment
Labels: bug, moreinfo

#1160 - Updating tiddit to v3.6.1

Pull Request - State: closed - Opened by asp8200 12 months ago - 1 comment

#1159 - Poster

Pull Request - State: closed - Opened by FriederikeHanssen 12 months ago - 1 comment

#1158 - Preprint

Pull Request - State: closed - Opened by FriederikeHanssen 12 months ago - 1 comment

#1157 - Move all vep args from ext.args to params.vep_custom_args

Pull Request - State: closed - Opened by maxulysse 12 months ago - 3 comments

#1156 - Missing plugin nf-amazon

Issue - State: open - Opened by zprobot 12 months ago - 3 comments
Labels: wontfix

#1155 - Restore proper rendering in usage.md

Pull Request - State: closed - Opened by maxulysse 12 months ago - 1 comment

#1154 - Varlociraptor calls

Pull Request - State: open - Opened by FriederikeHanssen 12 months ago - 2 comments

#1153 - Validate umi sentieon

Pull Request - State: closed - Opened by FriederikeHanssen 12 months ago - 1 comment

#1152 - Make patient optional in the samplesheet

Issue - State: open - Opened by saulpierotti 12 months ago - 10 comments
Labels: enhancement

#1151 - Refactor

Pull Request - State: closed - Opened by FriederikeHanssen 12 months ago - 2 comments

#1150 - Refactor

Pull Request - State: closed - Opened by FriederikeHanssen 12 months ago - 3 comments

#1149 - Fixing exome flag with Manta

Pull Request - State: closed - Opened by maxulysse 12 months ago - 1 comment

#1148 - Intervals BED file processing: remove headers and validate any timing information

Issue - State: open - Opened by tdanhorn 12 months ago
Labels: enhancement

#1147 - WIP: transfer mutect2 SBWFs to modules repo

Pull Request - State: open - Opened by maxulysse 12 months ago - 2 comments

#1146 - Better "error handling" around FilterVariantTranches

Issue - State: open - Opened by asp8200 12 months ago
Labels: enhancement

#1145 - Fix Zenodo Links

Pull Request - State: closed - Opened by maxulysse 12 months ago - 1 comment

#1144 - Filtering reads by mapping to multiple reference genome

Issue - State: closed - Opened by pmoris almost 1 year ago - 1 comment
Labels: enhancement

#1143 - snpeff_db a string not a number

Pull Request - State: closed - Opened by maxulysse almost 1 year ago - 4 comments

#1142 - Time course sampling analysis

Issue - State: open - Opened by frenkiboy about 1 year ago - 3 comments
Labels: enhancement

#1141 - Pass on the number of tumor samples per patient

Issue - State: open - Opened by berguner about 1 year ago
Labels: enhancement

#1140 - Important! Template update for nf-core/tools v2.9

Pull Request - State: closed - Opened by nf-core-bot about 1 year ago - 4 comments

#1139 - ERROR while running annotation step with vep

Issue - State: closed - Opened by FrancisNietzsche about 1 year ago - 3 comments
Labels: bug

#1138 - jar -> tar

Pull Request - State: closed - Opened by rhagenson about 1 year ago - 2 comments

#1137 - GenomicsDBImport : Mismatching intervals for input-vcf-files and bed-interval-file

Issue - State: closed - Opened by asp8200 about 1 year ago
Labels: bug, PR opened

#1136 - fix typo + resize pictures

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 1 comment

#1135 - Avoid redundant index generation in sentieon flow

Pull Request - State: closed - Opened by asp8200 about 1 year ago - 1 comment

#1134 - ERROR ~ Cannot invoke method startsWith() on null object

Issue - State: open - Opened by adbeggs about 1 year ago - 5 comments
Labels: bug, moreinfo

#1133 - ERROR: terminated for an unknown reason -- Likely it has been terminated by the external system

Issue - State: open - Opened by amnghn about 1 year ago - 1 comment
Labels: bug, moreinfo

#1132 - Fixing names of published dedup-related files

Pull Request - State: closed - Opened by asp8200 about 1 year ago - 1 comment

#1131 - Sentieon docs

Pull Request - State: closed - Opened by asp8200 about 1 year ago - 3 comments

#1130 - back to dev

Pull Request - State: closed - Opened by asp8200 about 1 year ago - 1 comment

#1129 - Release candidate 3.2.3

Pull Request - State: closed - Opened by asp8200 about 1 year ago - 1 comment

#1128 - CHORES: Prepare 3.2.3

Pull Request - State: closed - Opened by asp8200 about 1 year ago - 1 comment

#1127 - Sarek copies dbSNP for each invocation of HaplotypeCaller

Issue - State: open - Opened by Schmytzi about 1 year ago - 4 comments
Labels: bug

#1126 - Improve caching of test data

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 3 comments

#1124 - Joint calling with mpileup

Issue - State: open - Opened by amnghn about 1 year ago - 2 comments
Labels: enhancement

#1122 - FEAT: Use annotation-cache and update VEP to v110

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 1 comment

#1121 - Optimisation: Drop samtools index processes

Issue - State: open - Opened by matthdsm about 1 year ago - 4 comments
Labels: enhancement

#1117 - Pipeline doesn't properly use resource setting from custom.config, when starting analysis from --step variant_calling

Issue - State: closed - Opened by amizeranschi about 1 year ago - 9 comments
Labels: bug

#1116 - Allow existing GenomicsDb as input to incrementally update

Pull Request - State: open - Opened by FriederikeHanssen about 1 year ago - 1 comment

#1113 - Update public_aws_ecr profile and add test

Pull Request - State: open - Opened by adamrtalbot about 1 year ago - 4 comments

#1112 - back to dev

Pull Request - State: closed - Opened by asp8200 about 1 year ago - 1 comment

#1111 - added sentieon in diagrams

Pull Request - State: closed - Opened by nicorap about 1 year ago

#1110 - Use AWS cache Annotation Depot

Issue - State: closed - Opened by maxulysse about 1 year ago - 1 comment
Labels: enhancement

#1109 - fix bcftools mpileup

Pull Request - State: closed - Opened by FriederikeHanssen about 1 year ago - 3 comments

#1108 - FIX: Refactor prefix definition

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 3 comments

#1107 - update config

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 1 comment

#1106 - FEAT: Add slack notification for megatests

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 2 comments

#1105 - FIX: Remove params.tracedir

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 1 comment

#1104 - Don't run samtools mpileup when only tools mpileup is selected

Issue - State: closed - Opened by FriederikeHanssen about 1 year ago - 6 comments
Labels: bug

#1103 - Fix output docs to also have bcftools mpileup output

Issue - State: closed - Opened by FriederikeHanssen about 1 year ago
Labels: bug

#1102 - For joint variant calling, produce a final VCF file with filtered variants (those that PASS filters)

Issue - State: closed - Opened by amizeranschi about 1 year ago
Labels: bug, PR opened

#1101 - Remove redundant index computation for MD & version for MD Spark

Pull Request - State: closed - Opened by FriederikeHanssen about 1 year ago - 2 comments

#1100 - FIX: Deepvariant duplicate index

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 1 comment

#1099 - Fix bcftools mpileup

Issue - State: closed - Opened by amnghn about 1 year ago - 1 comment
Labels: enhancement

#1098 - FIX: Mutect2 subworkflow

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 1 comment

#1097 - Error with BAM_MERGE_INDEX when using bwa-mem2: Unsorted positions on sequence #4: 1260047 followed by 1259502

Issue - State: closed - Opened by amizeranschi about 1 year ago - 7 comments
Labels: bug, wontfix, docs, input validation

#1096 - Release candidate 3.2.2

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 1 comment

#1095 - CHORES: Prepare 3.2.2

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 1 comment

#1094 - Error reported at the `GATHERPILEUPSUMMARIES` step causing the workflow to abort

Issue - State: closed - Opened by jaybee84 about 1 year ago - 5 comments
Labels: bug

#1093 - Fix ascat manual test

Pull Request - State: closed - Opened by asp8200 about 1 year ago - 1 comment

#1092 - nf-core download sarek --outdir nf-core-sarek --container singularity --compress none --revision 3.2.1

Issue - State: closed - Opened by ChristianRohde about 1 year ago - 19 comments
Labels: bug

#1091 - FEAT: add nf-test

Pull Request - State: open - Opened by maxulysse about 1 year ago - 2 comments

#1090 - Duplicated parameter setting line in the main workflow

Issue - State: closed - Opened by SPPearce about 1 year ago - 1 comment

#1089 - FIX: Remove duplicated code

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 1 comment

#1088 - FEATURE: Non hidden files with -profile test

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 1 comment

#1087 - FIX: Fix default memory issue with gatk4/createsequencedictionary

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 3 comments

#1086 - The Singularity fails while attempting to pull a specific image required for offline usage of Sarek.

Issue - State: closed - Opened by Hadi90Eidgah about 1 year ago
Labels: bug

#1085 - GATK4_CREATESEQUENCEDICTIONARY memory misspecification

Issue - State: closed - Opened by mjakobs about 1 year ago - 5 comments

#1084 - Ensembl VEP is skipped when using custom a custom genome (--igenomes_ignore --genome null)

Issue - State: closed - Opened by amizeranschi about 1 year ago - 2 comments
Labels: bug

#1083 - Fatal error when downloading sarek pipeline v2.7.1

Issue - State: open - Opened by solcos about 1 year ago - 6 comments
Labels: bug

#1082 - FIX: patch more modules

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 4 comments

#1081 - Release candidate 3.2.1

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 1 comment

#1080 - CHORES: Prepare release 3.2.1

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 3 comments

#1079 - fix typo in profile name

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 1 comment

#1078 - FIX: update bgziptabix module

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 1 comment

#1077 - remove quay.io

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 4 comments

#1076 - Feature: BAM inputs to align step for re-alignment

Issue - State: open - Opened by adamrtalbot about 1 year ago - 4 comments
Labels: enhancement

#1075 - Test full is using wrong config name

Issue - State: closed - Opened by FriederikeHanssen about 1 year ago - 1 comment
Labels: bug

#1074 - Sentieon haplotyper refactored

Pull Request - State: closed - Opened by asp8200 about 1 year ago - 4 comments

GitHub / nf-core/sarek issues and pull requests