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Fixed conflicts and updated modulels for nf-core/tools version 2.11.1 #408

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Jan 16, 2024
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0b1e295
Template update for nf-core/tools version 2.10
nf-core-bot Sep 26, 2023
ce82ef6
Merge branch 'TEMPLATE' into dev_template
svarona Oct 31, 2023
977d069
Fixed notes
svarona Nov 2, 2023
a90a257
Fixed a header
svarona Nov 2, 2023
4976471
Fixed biocontainers
svarona Nov 2, 2023
66be601
Added missing change
svarona Nov 2, 2023
67f531e
Fixed quay.io
svarona Nov 2, 2023
0fd940b
removed quay.io from main.nf
svarona Nov 2, 2023
b6804f5
Fixed again quay.io
svarona Nov 2, 2023
9da284a
Fixed test2
svarona Nov 2, 2023
c3a677d
Fixed module
svarona Nov 2, 2023
ff372f7
mas test
svarona Nov 2, 2023
a507d99
removed duplicated line
svarona Dec 19, 2023
9e0a1c2
Template update for nf-core/tools version 2.11
nf-core-bot Dec 19, 2023
20dc34d
updated modules
saramonzon Dec 19, 2023
7f2923b
fixing modules call according to updates
saramonzon Dec 19, 2023
3bd897e
Fixed lint
svarona Dec 20, 2023
48f8032
Template update for nf-core/tools version 2.11.1
nf-core-bot Dec 20, 2023
55bfa3a
Merge branch 'TEMPLATE' into dev_template
svarona Dec 21, 2023
3c7778c
Merge branch 'TEMPLATE' into dev_template
svarona Dec 21, 2023
fa532f6
Fix prettier
svarona Dec 21, 2023
dcc56b2
pixed prettier
svarona Dec 21, 2023
bf5fd9d
Fixed some conflicts
svarona Dec 22, 2023
28ce0d2
Updated modules
svarona Dec 27, 2023
a8ce52a
Fixed quast process
svarona Dec 27, 2023
8d57896
Fixed quast for multiqc
svarona Dec 27, 2023
5d63daf
Fixed ref fasta channel
svarona Dec 27, 2023
96cdeb7
Fixed ref fasta channel
svarona Dec 27, 2023
cfea905
Fixed empty channels
svarona Dec 27, 2023
eb7a82d
Fixed mosdepth process
svarona Dec 27, 2023
6d5b405
Fixed empty fields
svarona Dec 27, 2023
ad5b38a
Fixed quast
svarona Dec 27, 2023
5ccac08
Fixed mosdepth
svarona Dec 27, 2023
78a4143
Fixed empty channels
svarona Dec 27, 2023
661ec68
Fixed fasta channel
svarona Dec 27, 2023
508e270
Fixed gff channel for empty path
svarona Dec 27, 2023
566837a
Fixed prettier
svarona Dec 28, 2023
bb66560
Fixed empty channels
svarona Dec 28, 2023
b3d2dbb
Download medaka model for nanopore test
svarona Jan 15, 2024
249146a
Removed TODO comment
svarona Jan 16, 2024
4c850ba
Removed igenomes_base
svarona Jan 16, 2024
8df9b78
removed igenomes_base from validationSchemaIgnoreParams
svarona Jan 16, 2024
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Fixed empty channels
  • Loading branch information
svarona committed Dec 27, 2023
commit cfea905f51e67e19b7875bd916a0048e734c0e37
6 changes: 3 additions & 3 deletions subworkflows/local/snpeff_snpsift.nf
Original file line number Diff line number Diff line change
Expand Up @@ -28,9 +28,9 @@ workflow SNPEFF_SNPSIFT {

VCF_BGZIP_TABIX_STATS (
SNPEFF_ANN.out.vcf,
[],
[],
[]
[ [:], [] ],
[ [:], [] ],
[ [:], [] ]
)
ch_versions = ch_versions.mix(VCF_BGZIP_TABIX_STATS.out.versions)

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6 changes: 3 additions & 3 deletions subworkflows/local/variants_ivar.nf
Original file line number Diff line number Diff line change
Expand Up @@ -60,9 +60,9 @@ workflow VARIANTS_IVAR {

VCF_TABIX_STATS (
BCFTOOLS_SORT.out.vcf,
[],
[],
[]
[ [:], [] ],
[ [:], [] ],
[ [:], [] ]
)
ch_versions = ch_versions.mix(VCF_TABIX_STATS.out.versions)

Expand Down