nf-core/bamtofastq: Changelog The format is based on Keep a Changelog
and this project adheres to Semantic Versioning .
#108 - Setup nf-test and convert default and cram test to nf-test#110 - Convert chr tests to nf-test#110 - Convert no_bai and no_crai tests to nf-test#112 - Convert collate_fast, no_stats and no_qc tests to nf-test#114 - Add contributors to nextflow.config#120 - Add fastqutils/info to check for truncated or quality-mismatched files#122 - Add @FriederikeHanssen @maxulysse @famosab as CODEOWNERS
#90 - Template update for nf-core/tools v2.14.0#91 - Template update for nf-core/tools v2.14.1#93 , #94 - Update samtools to v1.20#90 - Template update for nf-core/tools v3.0.1#107 - Template update for nf-core/tools v3.2.1#110 - Update nf-test GHA#115 - Update modules cat/fastq, fastqc and multiqc#116 - Update samtools to v1.21#119 - Update samtools version in local module to v1.21#123 - Prepare release 2.2.0#128 - Template update for nf-core/tools v3.3.1
#109 - Fix snapshots#118 - Edit pattern for fasta_fai check#125 - Address review comments for release 2.2.0
Dependency
Old version
New version
cat
8.3
9.5
fastq_utils
-
0.25.2
MultiQC
1.21
1.28
Samtools
1.19.2
1.21
#73 Template update for nf-core/tools v2.12#75 , #78 Template update for nf-core/tools v2.13#80 , #84 Template update for nf-core/tools v2.13.1
#74 Update samtools to v1.19.2#76 Update modules cat/fastq and samtools/view#88 Update subworkflow utils_nfcore_pipeline
#77 Fix detection of paired-end or single-end for input with less than 1000 reads#81 Add function getGenomeAttribute to main.nf and remove it from subworkflows/local/utils_nfcore_bamtofastq_pipeline/main.nf
Dependency
Old version
New version
Samtools
1.17
1.19.2
MultiQC
1.15
1.21
#61 Template update for nf-core/tools v2.9#64 Template update for nf-core/tools v2.10
#63 Replace extract_csv with nf-validation plugin
#62 Adjust subway map for dark mode.
Dependency
Old version
New version
MultiQC
1.14
1.15
Initial release of nf-core/bamtofastq, created with the nf-core template.
#49 Add descriptions to main options#48 Add igenomes#45 Add test.yml files with md5sums#44 DSL2 conversion
#55 Code review suggestions & formatting#54 Code review changes#53 Code review & updated modules#52 Code review changed resources in configs#47 Template update for nf-core/tools v2.8
#49 Fixed release version#45 Minor bugfix with chromosome extraction
Dependency
Old version
New version
multiqc1.9
1.14
samtools1.10
1.17
Option --cram_files not needed anymore due to automatic format detection.
#36 Add options --cram_files and --reference_fasta to add support for CRAM files.#31 Add option --samtools_collate_fast and improve speed of cat.#32 Added --samtools_collate_fast to sortExtractMapped and changed cat command to append.#33 Added flag --reads_in_memory to specify how many reads shall be stored in memory.
v1.1.0 - Katherine Johnson
#21 Allows bam indices as additional input files#23 Fix documentation: --bam is --input now#23 Make stats computation optional with parameter --no_stats. Use at own risk.#26 BAM index is now also used for processes dealing with separating reads based on the mapping status of both mates
Initial release of qbic-pipelines/bamtofastq, created with the nf-core template.