new module - bamstats generalstats #4474
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ggabernet
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Nov 29, 2023
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Hi @johnoooh @ggabernet, I created #3193 at the Hackaton in March last year. Now I see this PR (thanks @johnoooh). Do you guys think we can get this merged during this hackaton? Many thanks! Emilio |
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Co-authored-by: Gisela Gabernet <[email protected]>
vlebars
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* initial commit * commit to test * added :: * changed md5 * back to : * added comments and md5 * removed . * added bamstats to a line * spaces after colons * colon issues * sed tests * sed changes * sed fix * ' fix * sed fix * uising back * fix removed * sed fixed hopefully * md5 fix * removed todo * documentation added to meta.yml * removed todos * removed todo * fixed whitespace * fix licence * whitespace * whitespace again * para change * para change * md5 change * Update modules/nf-core/bamstats/generalstats/main.nf Co-authored-by: Gisela Gabernet <[email protected]> * todo removed * nf-test conversion * Fix bamstats module test.yml * Migrate bamstats tests to nf-test * Update bamstats/generalstats module and tests --------- Co-authored-by: Gisela Gabernet <[email protected]> Co-authored-by: Emilio Palumbo <[email protected]>
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* master: Added contrast limited adaptive histogram equalization module (nf-core#5268) Leviosam2 index (nf-core#5316) Add subworkflow mapAD (nf-core#5239) Remove AMRFinderPlus DB update on each invocation (nf-core#5232) Revert "add paths in output directive in cellranger cout module" (nf-core#5306) Revert "update kallistobustools count output list" (nf-core#5307) Igv reports (nf-core#5263) Remove unnecessary .view() in subworkflows/nf-core/vcf_phase_shapeit5 & tests/modules/nf-core/shapeit5/ligate/main.nf (nf-core#5280) Add wittyer as module (nf-core#5171) Bamstats (nf-core#4474) gatk4_asereadcounter add updated meta and nf-tests (nf-core#5164) 4557 new module kaijumergeoutputs + stub Kraken2/Kraken2 (nf-core#5249) add cram/index support to bwamem2 (nf-core#5248) Add README to modules build with Docker (nf-core#4935) update paths for VEP (nf-core#5281) nf-test bases2fastq (nf-core#5272) Add module seqfu/stats (nf-core#5275)
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* master: Added contrast limited adaptive histogram equalization module (nf-core#5268) Leviosam2 index (nf-core#5316) Add subworkflow mapAD (nf-core#5239) Remove AMRFinderPlus DB update on each invocation (nf-core#5232) Revert "add paths in output directive in cellranger cout module" (nf-core#5306) Revert "update kallistobustools count output list" (nf-core#5307) Igv reports (nf-core#5263) Remove unnecessary .view() in subworkflows/nf-core/vcf_phase_shapeit5 & tests/modules/nf-core/shapeit5/ligate/main.nf (nf-core#5280) Add wittyer as module (nf-core#5171) Bamstats (nf-core#4474) gatk4_asereadcounter add updated meta and nf-tests (nf-core#5164) 4557 new module kaijumergeoutputs + stub Kraken2/Kraken2 (nf-core#5249) add cram/index support to bwamem2 (nf-core#5248) Add README to modules build with Docker (nf-core#4935) update paths for VEP (nf-core#5281) nf-test bases2fastq (nf-core#5272) Add module seqfu/stats (nf-core#5275) Added gt/gff3validator (nf-core#4718) Added liftoff (nf-core#5209)
tucano
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Mar 20, 2024
* initial commit * commit to test * added :: * changed md5 * back to : * added comments and md5 * removed . * added bamstats to a line * spaces after colons * colon issues * sed tests * sed changes * sed fix * ' fix * sed fix * uising back * fix removed * sed fixed hopefully * md5 fix * removed todo * documentation added to meta.yml * removed todos * removed todo * fixed whitespace * fix licence * whitespace * whitespace again * para change * para change * md5 change * Update modules/nf-core/bamstats/generalstats/main.nf Co-authored-by: Gisela Gabernet <[email protected]> * todo removed * nf-test conversion * Fix bamstats module test.yml * Migrate bamstats tests to nf-test * Update bamstats/generalstats module and tests --------- Co-authored-by: Gisela Gabernet <[email protected]> Co-authored-by: Emilio Palumbo <[email protected]>
jennylsmith
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* initial commit * commit to test * added :: * changed md5 * back to : * added comments and md5 * removed . * added bamstats to a line * spaces after colons * colon issues * sed tests * sed changes * sed fix * ' fix * sed fix * uising back * fix removed * sed fixed hopefully * md5 fix * removed todo * documentation added to meta.yml * removed todos * removed todo * fixed whitespace * fix licence * whitespace * whitespace again * para change * para change * md5 change * Update modules/nf-core/bamstats/generalstats/main.nf Co-authored-by: Gisela Gabernet <[email protected]> * todo removed * nf-test conversion * Fix bamstats module test.yml * Migrate bamstats tests to nf-test * Update bamstats/generalstats module and tests --------- Co-authored-by: Gisela Gabernet <[email protected]> Co-authored-by: Emilio Palumbo <[email protected]>
alexnater
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* initial commit * commit to test * added :: * changed md5 * back to : * added comments and md5 * removed . * added bamstats to a line * spaces after colons * colon issues * sed tests * sed changes * sed fix * ' fix * sed fix * uising back * fix removed * sed fixed hopefully * md5 fix * removed todo * documentation added to meta.yml * removed todos * removed todo * fixed whitespace * fix licence * whitespace * whitespace again * para change * para change * md5 change * Update modules/nf-core/bamstats/generalstats/main.nf Co-authored-by: Gisela Gabernet <[email protected]> * todo removed * nf-test conversion * Fix bamstats module test.yml * Migrate bamstats tests to nf-test * Update bamstats/generalstats module and tests --------- Co-authored-by: Gisela Gabernet <[email protected]> Co-authored-by: Emilio Palumbo <[email protected]>
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PR checklist
Closes #3193
There are several tools named Bamstats, I have used this one before so I thought it fit to add.