nf-core/fetchngs issues and pull requests

#135 - Dev -> Master for v1.9 release

Pull Request - State: closed - Opened by drpatelh about 2 years ago - 1 comment

#134 - Add '--nf_core_rnaseq_strandedness' parameter and support for nf-core/atacseq

Pull Request - State: closed - Opened by drpatelh about 2 years ago - 1 comment

#133 - Important! Template update for nf-core/tools v2.7.2

Pull Request - State: closed - Opened by nf-core-bot about 2 years ago - 1 comment

#132 - increased prefetch max download size

Pull Request - State: closed - Opened by kafkasl about 2 years ago - 1 comment

#131 - Important! Template update for nf-core/tools v2.7.1

Pull Request - State: closed - Opened by nf-core-bot about 2 years ago - 1 comment

#130 - Errors downloading scrnaseq data using Amazon Genomics CLI (version 1.5.2)

Issue - State: closed - Opened by jhgraber about 2 years ago - 1 comment
Labels: bug

#129 - Pipeline is working with SRA run IDs, but failing with corresponding Biosample IDs

Issue - State: closed - Opened by amizeranschi about 2 years ago - 10 comments
Labels: bug

#128 - nf-test

Pull Request - State: closed - Opened by Emiller88 about 2 years ago - 2 comments

#127 - Bump pipeline version to 1.9dev

Pull Request - State: closed - Opened by drpatelh about 2 years ago - 1 comment

#126 - Dev -> Master for v1.8 release

Pull Request - State: closed - Opened by drpatelh about 2 years ago - 1 comment

#125 - Fix #119

Pull Request - State: closed - Opened by drpatelh about 2 years ago - 1 comment

#124 - Fix #114

Pull Request - State: closed - Opened by drpatelh about 2 years ago - 1 comment

#123 - add a tower.yml

Pull Request - State: closed - Opened by pinin4fjords about 2 years ago - 6 comments

#122 - Tower yml

Pull Request - State: closed - Opened by pinin4fjords about 2 years ago - 1 comment

#121 - Add tower.yml to render samplesheet as Report in Tower

Issue - State: closed - Opened by pinin4fjords about 2 years ago - 2 comments
Labels: enhancement

#120 - Single text input field for project-level identifiers

Issue - State: open - Opened by pinin4fjords about 2 years ago - 3 comments
Labels: enhancement

#119 - --force_sratools_download results in different fastq names compared to FTP download

Issue - State: closed - Opened by ojziff about 2 years ago - 1 comment
Labels: bug

#118 - Allow input pattern validation for csv/tsv/txt

Issue - State: closed - Opened by ojziff over 2 years ago - 3 comments
Labels: enhancement

#117 - eutils rate limits exceeded (with relatively small input set of accessions)

Issue - State: open - Opened by adf-ncgr over 2 years ago - 4 comments
Labels: bug

#116 - Mixture of ids provided via --input: Please provide either SRA / ENA / DDBJ or Synapse ids!

Issue - State: closed - Opened by royfrancis over 2 years ago - 6 comments
Labels: bug

#115 - Important! Template update for nf-core/tools v2.6

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago - 2 comments

#114 - Final samplesheet is not created when --skip_fastq_download is provided

Issue - State: closed - Opened by SchwarzMarek over 2 years ago - 2 comments
Labels: bug

#113 - Important! Template update for nf-core/tools v2.5.1

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago - 1 comment

#112 - Important! Template update for nf-core/tools v2.5

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago - 2 comments

#111 - Change input mimetype to csv

Issue - State: closed - Opened by drpatelh over 2 years ago - 1 comment
Labels: enhancement

#110 - Use ffq to fetch id metadata

Issue - State: open - Opened by drpatelh over 2 years ago
Labels: enhancement

#109 - Problem executing `sra_ids_to_runinfo.py`: KeyError: 'Experiment'

Issue - State: closed - Opened by telatin over 2 years ago - 3 comments
Labels: bug

#108 - Can SRA responses be trapped and reported in a user-friendly manner?

Issue - State: open - Opened by telatin over 2 years ago - 1 comment
Labels: enhancement

#107 - Downloading of controlled data

Issue - State: closed - Opened by JiaGengChang over 2 years ago - 3 comments
Labels: enhancement

#106 - Test fails with singularity profile

Issue - State: closed - Opened by el239 over 2 years ago - 4 comments
Labels: bug

#105 - Bump pipeline version to 1.8dev

Pull Request - State: closed - Opened by drpatelh over 2 years ago - 2 comments

#104 - Add GEO support

Issue - State: closed - Opened by drpatelh over 2 years ago - 1 comment
Labels: enhancement

#103 - Dev -> Master for v1.7 release

Pull Request - State: closed - Opened by drpatelh over 2 years ago - 1 comment

#102 - Fix breaking changes introduced in the NCBI API

Pull Request - State: closed - Opened by drpatelh over 2 years ago - 5 comments

#101 - Test fails when running with singularity

Issue - State: closed - Opened by el239 over 2 years ago - 2 comments
Labels: bug

#100 - Implement ffq

Pull Request - State: open - Opened by drpatelh over 2 years ago - 2 comments

#99 - SRA_IDS_TO_RUNINFO fails due to bad request

Issue - State: closed - Opened by dmalzl over 2 years ago - 2 comments
Labels: bug

#98 - some samples fail with --force_sratools_download due to changes in prefetch results

Issue - State: closed - Opened by dmalzl over 2 years ago - 13 comments
Labels: bug

#97 - Add taxprofiler support for --nf_core_pipeline

Pull Request - State: closed - Opened by jfy133 over 2 years ago - 1 comment

#96 - Add taxprofiler samplesheet generation support

Issue - State: closed - Opened by jfy133 over 2 years ago
Labels: enhancement

#95 - add --save_merged_fastq for merging technical repeats to fetchngs

Issue - State: open - Opened by ojziff over 2 years ago - 5 comments
Labels: enhancement

#94 - Bump pipeline version to 1.7dev

Pull Request - State: closed - Opened by drpatelh over 2 years ago - 1 comment

#93 - fix: use parameter for publishing mode

Pull Request - State: closed - Opened by Midnighter over 2 years ago - 1 comment

#92 - Dev -> Master for 1.6 release

Pull Request - State: closed - Opened by drpatelh over 2 years ago - 4 comments

#91 - Follow up fixes to issue #57

Pull Request - State: closed - Opened by drpatelh over 2 years ago - 1 comment

#90 - Important! Template update for nf-core/tools v2.4

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago

#89 - refactor: use nf-core modules for sratools subworkflow

Pull Request - State: closed - Opened by Midnighter over 2 years ago - 3 comments

#88 - Test run for fetchngs failed

Issue - State: closed - Opened by dalinlee over 2 years ago - 2 comments
Labels: bug

#87 - Choice between fastq and fasterq-dump when using --force_sratools_download

Issue - State: closed - Opened by dmalzl over 2 years ago - 5 comments
Labels: enhancement

#86 - Wrong use of --progress in prefetch command leads to failure of pipeline

Issue - State: closed - Opened by dmalzl over 2 years ago - 17 comments
Labels: bug

#85 - Not able to fetch metadata for ERR* ids associated with ArrayExpress

Issue - State: closed - Opened by drpatelh over 2 years ago - 5 comments
Labels: enhancement

#84 - Replace vanilla Linux Biocontainer with Ubuntu

Pull Request - State: closed - Opened by drpatelh over 2 years ago - 1 comment

#82 - Important! Template update for nf-core/tools v2.3.2

Pull Request - State: closed - Opened by nf-core-bot almost 3 years ago

#81 - Important! Template update for nf-core/tools v2.3.1

Pull Request - State: closed - Opened by nf-core-bot almost 3 years ago - 1 comment

#80 - Add troubleshooting section and FTP alternative docs

Pull Request - State: closed - Opened by maxibor almost 3 years ago

#79 - Important! Template update for nf-core/tools v2.3

Pull Request - State: closed - Opened by nf-core-bot almost 3 years ago - 2 comments

#77 - Allow a prepared ENA metadata samplesheet as input

Issue - State: open - Opened by Midnighter almost 3 years ago - 1 comment
Labels: enhancement

#74 - support SRP/PRJNA input type

Issue - State: closed - Opened by kaitlinchaung almost 3 years ago
Labels: enhancement

#72 - The input file extension matters

Issue - State: closed - Opened by Midnighter almost 3 years ago - 1 comment
Labels: bug

#68 - support aspera download

Issue - State: open - Opened by atongsa about 3 years ago - 8 comments
Labels: enhancement

#67 - Important! Template update for nf-core/tools v2.2

Pull Request - State: closed - Opened by nf-core-bot about 3 years ago

#66 - Add support for prefetch argument `--max-size`

Issue - State: closed - Opened by jfy133 about 3 years ago - 7 comments
Labels: enhancement

#64 - Running sratools prefetch on Azure

Issue - State: closed - Opened by drpatelh about 3 years ago - 3 comments
Labels: bug

#57 - fetchngs fails if FTP is blocked

Issue - State: closed - Opened by kvn95ss about 3 years ago - 1 comment
Labels: documentation, enhancement

#32 - fetchngs pipeline not working on scRNAseq

Issue - State: closed - Opened by archieandrews10 over 3 years ago - 3 comments
Labels: bug

GitHub / nf-core/fetchngs issues and pull requests