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Hisat2-build: index construction w/ truly optional inputs #3649

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merged 8 commits into from
Jul 20, 2023
Merged

Hisat2-build: index construction w/ truly optional inputs #3649

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491947c
index construction mode dependent on optional inputs rather than memo…
JackCurragh Jul 18, 2023
28d1061
added tests for new functionality
JackCurragh Jul 19, 2023
15e1cce
updated tests to use appropriate test data
JackCurragh Jul 19, 2023
73557a2
Merge branch 'master' into hisat2_build_update
JackCurragh Jul 19, 2023
b8cec46
cleaned up test.yml to only contain BUILD outputs
JackCurragh Jul 19, 2023
3a5a18d
Merge branch 'master' into hisat2_build_update
jfy133 Jul 19, 2023
eb60996
removed unnecessary extract ss call
JackCurragh Jul 20, 2023
4942497
added : to empty metamaps. Reverted to sarscov2 test files
JackCurragh Jul 20, 2023
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6 changes: 3 additions & 3 deletions modules/nf-core/hisat2/build/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -37,9 +37,9 @@ process HISAT2_BUILD {
def hisat2_build_memory = params.hisat2_build_memory ? (params.hisat2_build_memory as nextflow.util.MemoryUnit).toGiga() : 0
if (avail_mem >= hisat2_build_memory) {
log.info "[HISAT2 index build] At least ${hisat2_build_memory} GB available, so using splice sites and exons to build HISAT2 index"
extract_exons = "hisat2_extract_exons.py $gtf > ${gtf.baseName}.exons.txt"
ss = "--ss $splicesites"
exon = "--exon ${gtf.baseName}.exons.txt"
extract_exons = gtf ? "hisat2_extract_exons.py $gtf > ${gtf.baseName}.exons.txt" : ""
ss = splicesites ? "--ss $splicesites" : ""
exon = gtf ? "--exon ${gtf.baseName}.exons.txt" : ""
} else {
log.info "[HISAT2 index build] Less than ${hisat2_build_memory} GB available, so NOT using splice sites and exons to build HISAT2 index."
log.info "[HISAT2 index build] Use --hisat2_build_memory [small number] to skip this check."
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21 changes: 21 additions & 0 deletions tests/modules/nf-core/hisat2/build_test/main.nf
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Expand Up @@ -15,3 +15,24 @@ workflow test_hisat2_build {
HISAT2_EXTRACTSPLICESITES ( gtf )
HISAT2_BUILD ( fasta, gtf, HISAT2_EXTRACTSPLICESITES.out.txt )
}

workflow test_hisat2_build_fasta_only {
fasta = [ [id:'genome'],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
gtf = [ [id:'genome'],
file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
]
HISAT2_BUILD ( fasta, [[:],[]], [[:],[]] )
}

workflow test_hisat2_build_fasta_ss_only {
fasta = [ [id:'genome'],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
gtf = [ [id:'genome'],
file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
]
HISAT2_EXTRACTSPLICESITES ( gtf )
HISAT2_BUILD ( fasta, [[:],[]], HISAT2_EXTRACTSPLICESITES.out.txt )
}
60 changes: 54 additions & 6 deletions tests/modules/nf-core/hisat2/build_test/test.yml
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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
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