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Marie lataretu/issue55 #70

Merged
merged 65 commits into from
Dec 14, 2023
Merged

Marie lataretu/issue55 #70

merged 65 commits into from
Dec 14, 2023

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MarieLataretu
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MarieLataretu and others added 30 commits May 17, 2022 17:33
@MarieLataretu
initial commit
3dce486
@MarieLataretu
check for bgzipped files
9dc3449
@MarieLataretu
added pysam
7f40ca8
@MarieLataretu
output also bams
f8c3dfc
@MarieLataretu
split bam by name list
5715b05
@MarieLataretu
output index
84756d9
@MarieLataretu
added split fastq
fdeb92f
@MarieLataretu
split cleaned fastqs
1384cfd
@MarieLataretu
split fastq by read names
9f93ec4
@MarieLataretu
mv keep to extra wf
68972e0
@MarieLataretu
publish correct fastqs
9c2b5ce
@MarieLataretu
rm unused stuff
74d8bbf
@MarieLataretu
fixed bug for fasta input
fa3113f
@MarieLataretu
rm view
281171e
@MarieLataretu
added publish mode param
e1dbf5d
@MarieLataretu
emit both bams
77fa2cf
@MarieLataretu
added typle for bam tuple
78015a3
@MarieLataretu
update publish
d262bb8
@MarieLataretu
added type to bam
562923e
@MarieLataretu
update publish
a0a5e99
@MarieLataretu
renamed output
dea952b
@MarieLataretu
added type
12e3ce4
@MarieLataretu
update publish
06b817e
@MarieLataretu
updated publish
c2e3359
@MarieLataretu
added name
c0c1a20
@MarieLataretu
works now for multiple sampes
2ed4e93
@MarieLataretu
updated workflow figure
001cbd6
@MarieLataretu
Merge branch 'dev' into MarieLataretu/issue55
ca353fd
@MarieLataretu
Merge branch 'dev' into MarieLataretu/issue55
86b3502
@matthuska
Fix some incorrect output names, conda envs, container for pigz
b3df249
matthuska and others added 28 commits November 16, 2023 13:25
@matthuska
Place fastq files that map to 'keep' genome and to the host/control/o…
df2497e 
…wn/rrna 'remove' genomes in appropriate intermediate folders
@matthuska
Re-publish multiqc report to the qc/ directory (by default)
f739f8b
@matthuska
Only publish sorted.bam{,.bai} intermediate bam files
b2ec355
@matthuska
Publish idxstats and flagstats so they are next to their bam files
d91f94f
@matthuska
Handle --strict_dcs and --min_clip output in results dir
82b60c0
@matthuska
First steps towards making illumina/bbduk results dir look right
fc1318b
@matthuska
Add bed_samtools container bump minimap2 container (from main)
f03c8a5
@matthuska
--keep is now working with bbduk. results/ is properly populated.
619c205
@matthuska
Add seqkit conda environment file
4611647
@matthuska
Output fasta when input is fasta
e5e5659 
Also remove dead code, skip creation of uncompressed fast[aq] file by letting
samtools directly write a gzipped file. Remove whitespace at end of some lines.
@matthuska
Add --no_intermediate argument to skip publishing intermediate files …
753f97c 
…to results/
@matthuska
Add singularity/ dir to .gitignore
bb499ac
@matthuska
Tweak filter_fastq_by_name to work properly, avoid reading and writin…
14840fb 
…g to the same file in a pipe
@matthuska
Replace scary zcat/paste/grep/tr with seqkit grep
bb074a7
@matthuska
Add clarifying comments to the filter_fastq_by_name process
40276ea
@matthuska
Remove overwrite: false from publishDir directives
dc59d28
@MarieLataretu
fix stub touch
39bd52e 
- output is expecting the suffix .sorted.bam
@MarieLataretu
added seqkit to citations
d29a5ef
Add -keep to help mssg. Reformated --help a bit. Removed old profiles…
d2ae118 
… for ARA and EBI.
adjusted the README a bit
95ce2ee
change sed command for --keep and add empty BED channel for phix control
975e05a
@matthuska
Publish host genome and index for loading into IGV. Skipped if interm…
814e37b 
…ediate files are skipped.
@matthuska
Switch to seqkit for check_own and concat_contamination
5d87ac4
bump seqkit container
4228c4b
@matthuska
Update fastq_from_bam to publish illumina data properly. Regexes are …
26bd1d0 
…geting crazy, need to rethink this.
@matthuska
Merge pull request #67 from hoelzer/feature/reorganize-results
c22c7c1 
Reorganize the results directory
@MarieLataretu
Merge branch 'dev' into MarieLataretu/issue55
dea8a3e
@MarieLataretu
linked to correct workflow figure
f50812e
@MarieLataretu MarieLataretu merged commit 29a7c8b into dev Dec 14, 2023
@MarieLataretu MarieLataretu deleted the MarieLataretu/issue55 branch January 4, 2024 11:18
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2 participants
@MarieLataretu @matthuska