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nf-core_modules/modules/samtools
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nickhsmith 454e0acc09
Mpileup intervals (#1955) 
* update tests

* update

* update

* make the manta inputs consistant for germline/somatic/tumoronly

* match chromosomes to cram file (chr21)

* undo genotypegvfs

* undo genotypegvfs

* include intervals

* update md5 with interval

Co-authored-by: Smith Nicholas <smith@in.tum.de>
2022-08-16 14:16:35 +02:00
..
ampliconclip Improve descriptions for modules with missing 2022-07-06 12:03:08 +02:00
bam2fq Test --no-name to solve inconsistent checksums 2022-05-03 15:18:09 +02:00
collatefastq Add samtools/collatefastq module (#1536) 2022-04-20 10:05:17 +02:00
convert rename aligned to alignment 2022-05-09 16:07:49 +02:00
depth Samtools version update (#1507) 2022-04-11 14:26:28 +02:00
dict Added the samtools/dict module (#1922) 2022-07-26 22:13:19 +01:00
faidx Added support for ext.args in samtools/faidx (#1919) 2022-07-26 21:51:47 +01:00
fastq Samtools version update (#1507) 2022-04-11 14:26:28 +02:00
fixmate Samtools version update (#1507) 2022-04-11 14:26:28 +02:00
flagstat samtools/*stats*: use prefix for outputs (#1788) 2022-06-16 13:42:01 +02:00
idxstats samtools/*stats*: use prefix for outputs (#1788) 2022-06-16 13:42:01 +02:00
index Samtools version update (#1507) 2022-04-11 14:26:28 +02:00
merge small update to samtools/merge (#1896) 2022-07-18 11:37:45 +02:00
mpileup Mpileup intervals (#1955) 2022-08-16 14:16:35 +02:00
sort Samtools version update (#1507) 2022-04-11 14:26:28 +02:00
stats more generic name because of multiple extension (#1880) 2022-07-14 11:42:00 +02:00
view feat added stub to modules 2022-05-02 10:34:14 +02:00