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Fgbio tmpdir modification #1890

Merged
merged 14 commits into from
Jul 15, 2022
Merged

Fgbio tmpdir modification #1890

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9cae51e
Updated container versions for fgbio groupreadsbyumi and callmolecula…
WackerO Jul 13, 2022
900218c
Merge branch 'nf-core:master' into master
WackerO Jul 14, 2022
298c9b6
Corrected fgbio call container, trying to fix fgbio group tests
WackerO Jul 14, 2022
b02075c
Merge branch 'master' of https://github.com/nf-core/modules
WackerO Jul 14, 2022
6a653f7
Removed incorrect line
WackerO Jul 14, 2022
7de8719
Merge branch 'master' of https://github.com/nf-core/modules
WackerO Jul 14, 2022
caa369b
Merge branch 'master' of https://github.com/nf-core/modules
WackerO Jul 15, 2022
da4782f
Changed tmp-dir to .
WackerO Jul 15, 2022
458e206
Update modules/fgbio/groupreadsbyumi/main.nf
WackerO Jul 15, 2022
9b1f47b
Update modules/fgbio/fastqtobam/main.nf
WackerO Jul 15, 2022
fff912b
Added callmol and sortbam
WackerO Jul 15, 2022
f47ccf2
Merge branch 'fgbio_error' of https://github.com/WackerO/modules into…
WackerO Jul 15, 2022
de08233
fixed typo in callmol container
WackerO Jul 15, 2022
e98c9cb
Merge branch 'master' of https://github.com/nf-core/modules into fgbi…
WackerO Jul 15, 2022
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2 changes: 1 addition & 1 deletion modules/fgbio/fastqtobam/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ process FGBIO_FASTQTOBAM {
mkdir tmp
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fgbio \\
--tmp-dir=${PWD}/tmp \\
--tmp-dir=. \\
FastqToBam \\
-i $reads \\
-o "${prefix}_umi_converted.bam" \\
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2 changes: 1 addition & 1 deletion modules/fgbio/groupreadsbyumi/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ process FGBIO_GROUPREADSBYUMI {
mkdir tmp
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fgbio \\
--tmp-dir=${PWD}/tmp \\
--tmp-dir=. \\
GroupReadsByUmi \\
-s $strategy \\
$args \\
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