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Hisat2-build: index construction w/ truly optional inputs (#3649)
* index construction mode dependent on optional inputs rather than memory availability * added tests for new functionality * updated tests to use appropriate test data * cleaned up test.yml to only contain BUILD outputs * removed unnecessary extract ss call * added : to empty metamaps. Reverted to sarscov2 test files --------- Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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Original file line number | Diff line number | Diff line change |
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@@ -1,23 +1,71 @@ | ||
- name: hisat2 build test_hisat2_build | ||
command: nextflow run ./tests/modules/nf-core/hisat2/build_test -entry test_hisat2_build -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hisat2/build/nextflow.config | ||
command: nextflow run ./tests/modules/nf-core/hisat2/build -entry test_hisat2_build -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hisat2/build/nextflow.config | ||
tags: | ||
- hisat2 | ||
- hisat2/build | ||
- hisat2 | ||
files: | ||
- path: output/hisat2/genome.splice_sites.txt | ||
- path: output/hisat2/hisat2/genome.1.ht2 | ||
md5sum: 057cfa8a22b97ee9cff4c8d342498803 | ||
- path: output/hisat2/hisat2/genome.2.ht2 | ||
md5sum: 47b153cd1319abc88dda532462651fcf | ||
- path: output/hisat2/hisat2/genome.3.ht2 | ||
md5sum: 4ed93abba181d8dfab2e303e33114777 | ||
- path: output/hisat2/hisat2/genome.4.ht2 | ||
md5sum: c25be5f8b0378abf7a58c8a880b87626 | ||
- path: output/hisat2/hisat2/genome.5.ht2 | ||
md5sum: 91198831aaba993acac1734138c5f173 | ||
- path: output/hisat2/hisat2/genome.6.ht2 | ||
md5sum: 265e1284ce85686516fae5d35540994a | ||
- path: output/hisat2/hisat2/genome.7.ht2 | ||
md5sum: 9013eccd91ad614d7893c739275a394f | ||
- path: output/hisat2/hisat2/genome.8.ht2 | ||
md5sum: 33cdeccccebe80329f1fdbee7f5874cb | ||
- path: output/hisat2/versions.yml | ||
|
||
- name: hisat2 build test_hisat2_build_fasta_only | ||
command: nextflow run ./tests/modules/nf-core/hisat2/build -entry test_hisat2_build_fasta_only -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hisat2/build/nextflow.config | ||
tags: | ||
- hisat2/build | ||
- hisat2 | ||
files: | ||
- path: output/hisat2/hisat2/genome.1.ht2 | ||
md5sum: 057cfa8a22b97ee9cff4c8d342498803 | ||
md5sum: 98284d11e09faba5be6caeacceae7b3c | ||
- path: output/hisat2/hisat2/genome.2.ht2 | ||
md5sum: 47b153cd1319abc88dda532462651fcf | ||
- path: output/hisat2/hisat2/genome.6.ht2 | ||
md5sum: 265e1284ce85686516fae5d35540994a | ||
- path: output/hisat2/hisat2/genome.3.ht2 | ||
md5sum: 4ed93abba181d8dfab2e303e33114777 | ||
- path: output/hisat2/hisat2/genome.4.ht2 | ||
md5sum: c25be5f8b0378abf7a58c8a880b87626 | ||
- path: output/hisat2/hisat2/genome.5.ht2 | ||
md5sum: 4db21638bce5ab535147c14a8c5ed27b | ||
- path: output/hisat2/hisat2/genome.6.ht2 | ||
md5sum: 265e1284ce85686516fae5d35540994a | ||
- path: output/hisat2/hisat2/genome.7.ht2 | ||
md5sum: 9013eccd91ad614d7893c739275a394f | ||
- path: output/hisat2/hisat2/genome.8.ht2 | ||
md5sum: 33cdeccccebe80329f1fdbee7f5874cb | ||
- path: output/hisat2/versions.yml | ||
|
||
- name: hisat2 build test_hisat2_build_fasta_ss_only | ||
command: nextflow run ./tests/modules/nf-core/hisat2/build -entry test_hisat2_build_fasta_ss_only -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hisat2/build/nextflow.config | ||
tags: | ||
- hisat2/build | ||
- hisat2 | ||
files: | ||
- path: output/hisat2/hisat2/genome.1.ht2 | ||
md5sum: 057cfa8a22b97ee9cff4c8d342498803 | ||
- path: output/hisat2/hisat2/genome.2.ht2 | ||
md5sum: 47b153cd1319abc88dda532462651fcf | ||
- path: output/hisat2/hisat2/genome.3.ht2 | ||
md5sum: 4ed93abba181d8dfab2e303e33114777 | ||
- path: output/hisat2/hisat2/genome.4.ht2 | ||
md5sum: c25be5f8b0378abf7a58c8a880b87626 | ||
- path: output/hisat2/hisat2/genome.5.ht2 | ||
md5sum: 91198831aaba993acac1734138c5f173 | ||
- path: output/hisat2/hisat2/genome.6.ht2 | ||
md5sum: 265e1284ce85686516fae5d35540994a | ||
- path: output/hisat2/hisat2/genome.7.ht2 | ||
md5sum: 9013eccd91ad614d7893c739275a394f | ||
- path: output/hisat2/hisat2/genome.8.ht2 | ||
md5sum: 33cdeccccebe80329f1fdbee7f5874cb | ||
- path: output/hisat2/versions.yml |