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Update/input assure to accommodate changes in locidex mlst.json allele reports #28
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09efa91
Update locidex container registry
kylacochrane 9e820c8
Update input_assure.py to accomodate the revised Locidex mlst.json re…
kylacochrane 29debe1
Update test data (reports and samplesheets) to accomodate the revised…
kylacochrane 2cb4888
Update paths to mlst files in samplesheet.csv
kylacochrane cc1444b
Fixed error in samplesheet
kylacochrane 9a87a2b
Fixed typo
kylacochrane 307aa82
Updated container registry handling
kylacochrane 29d427f
add user UID/GID to Nextflow Docker run in CI to fix getpwuid() error
kylacochrane 09cfa2b
add root user to Nextflow Docker run in CI to fix getpwuid() error
kylacochrane 2639645
Updated container for arborview
kylacochrane 726d2c9
Refactor user configuration for locidex module: Remove --user specs f…
kylacochrane 8a016b4
Revert to previous user config in ci.yml
kylacochrane eac46d8
Update --user in ci.yml
kylacochrane db503bf
Removed --user configurations for locidex
kylacochrane 1aebb70
Updated CHANGELOG.md
kylacochrane f3f83cd
Updated release version
kylacochrane a23379c
Removed print debugging statement in input_assure.py
kylacochrane 6f7f59d
Replace unsorted list with sorted() for consistent ordering in input_…
kylacochrane f787028
Update locidex to version 0.2.3
kylacochrane cf5248e
Add link to release tag
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,4 +1,4 @@ | ||
sample,mlst_alleles | ||
sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample1.mlst.json | ||
sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample2.mlst.json | ||
sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample3.mlst.json | ||
sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample1.mlst.json | ||
sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample2.mlst.json | ||
sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample3.mlst.json |
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Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -178,6 +178,9 @@ docker.registry = 'quay.io' | |
podman.registry = 'quay.io' | ||
singularity.registry = 'quay.io' | ||
|
||
// Override the default Docker registry when required | ||
process.ext.override_configured_container_registry = true | ||
|
||
// Nextflow plugins | ||
plugins { | ||
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet | ||
|
@@ -226,7 +229,7 @@ manifest { | |
description = """IRIDA Next Genomic Address Service Clustering Pipeline""" | ||
mainScript = 'main.nf' | ||
nextflowVersion = '!>=23.04.0' | ||
version = '0.2.0' | ||
version = '0.3.0' | ||
doi = '' | ||
defaultBranch = 'main' | ||
} | ||
|
22 changes: 18 additions & 4 deletions
22
tests/data/reports/case-hamming/sample1.mlst.subtyping.json
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,7 +1,21 @@ | ||
{ | ||
"sample1": { | ||
"l1": "1", | ||
"l2": "1", | ||
"l3": "1" | ||
"db_info": {}, | ||
"parameters": { | ||
"mode": "normal", | ||
"min_match_ident": 100, | ||
"min_match_cov": 100, | ||
"max_ambiguous": 0, | ||
"max_internal_stops": 0 | ||
}, | ||
"data": { | ||
"sample_name": "sample1", | ||
"profile": { | ||
"sample1": { | ||
"l1": "1", | ||
"l2": "1", | ||
"l3": "1" | ||
} | ||
}, | ||
"seq_data": {} | ||
} | ||
} |
22 changes: 18 additions & 4 deletions
22
tests/data/reports/case-hamming/sample2.mlst.subtyping.json
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,7 +1,21 @@ | ||
{ | ||
"sample2": { | ||
"l1": "1", | ||
"l2": "2", | ||
"l3": "1" | ||
"db_info": {}, | ||
"parameters": { | ||
"mode": "normal", | ||
"min_match_ident": 100, | ||
"min_match_cov": 100, | ||
"max_ambiguous": 0, | ||
"max_internal_stops": 0 | ||
}, | ||
"data": { | ||
"sample_name": "sample2", | ||
"profile": { | ||
"sample2": { | ||
"l1": "1", | ||
"l2": "2", | ||
"l3": "1" | ||
} | ||
}, | ||
"seq_data": {} | ||
} | ||
} |
22 changes: 18 additions & 4 deletions
22
tests/data/reports/case-hamming/sample3.mlst.subtyping.json
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,7 +1,21 @@ | ||
{ | ||
"sample3": { | ||
"l1": "2", | ||
"l2": "1", | ||
"l3": "2" | ||
"db_info": {}, | ||
"parameters": { | ||
"mode": "normal", | ||
"min_match_ident": 100, | ||
"min_match_cov": 100, | ||
"max_ambiguous": 0, | ||
"max_internal_stops": 0 | ||
}, | ||
"data": { | ||
"sample_name": "sample3", | ||
"profile": { | ||
"sample3": { | ||
"l1": "2", | ||
"l2": "1", | ||
"l3": "2" | ||
} | ||
}, | ||
"seq_data": {} | ||
} | ||
} |
22 changes: 18 additions & 4 deletions
22
tests/data/reports/case-hash-missing/sample1.mlst.subtyping.json
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,7 +1,21 @@ | ||
{ | ||
"sample1": { | ||
"l1": "b026324c6904b2a9cb4b88d6d61c81d1", | ||
"l2": "b026324c6904b2a9cb4b88d6d61c81d1", | ||
"l3": "b026324c6904b2a9cb4b88d6d61c81d1" | ||
"db_info": {}, | ||
"parameters": { | ||
"mode": "normal", | ||
"min_match_ident": 100, | ||
"min_match_cov": 100, | ||
"max_ambiguous": 0, | ||
"max_internal_stops": 0 | ||
}, | ||
"data": { | ||
"sample_name": "sample1", | ||
"profile": { | ||
"sample1": { | ||
"l1": "b026324c6904b2a9cb4b88d6d61c81d1", | ||
"l2": "b026324c6904b2a9cb4b88d6d61c81d1", | ||
"l3": "b026324c6904b2a9cb4b88d6d61c81d1" | ||
} | ||
}, | ||
"seq_data": {} | ||
} | ||
} |
22 changes: 18 additions & 4 deletions
22
tests/data/reports/case-hash-missing/sample2.mlst.subtyping.json
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,7 +1,21 @@ | ||
{ | ||
"sample2": { | ||
"l1": "-", | ||
"l2": "26ab0db90d72e28ad0ba1e22ee510510", | ||
"l3": "b026324c6904b2a9cb4b88d6d61c81d1" | ||
"db_info": {}, | ||
"parameters": { | ||
"mode": "normal", | ||
"min_match_ident": 100, | ||
"min_match_cov": 100, | ||
"max_ambiguous": 0, | ||
"max_internal_stops": 0 | ||
}, | ||
"data": { | ||
"sample_name": "sample2", | ||
"profile": { | ||
"sample2": { | ||
"l1": "-", | ||
"l2": "26ab0db90d72e28ad0ba1e22ee510510", | ||
"l3": "b026324c6904b2a9cb4b88d6d61c81d1" | ||
} | ||
}, | ||
"seq_data": {} | ||
} | ||
} |
22 changes: 18 additions & 4 deletions
22
tests/data/reports/case-hash-missing/sample3-more-missing.mlst.subtyping.json
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,7 +1,21 @@ | ||
{ | ||
"sample3": { | ||
"l1": "-", | ||
"l2": "-", | ||
"l3": "26ab0db90d72e28ad0ba1e22ee510510" | ||
"db_info": {}, | ||
"parameters": { | ||
"mode": "normal", | ||
"min_match_ident": 100, | ||
"min_match_cov": 100, | ||
"max_ambiguous": 0, | ||
"max_internal_stops": 0 | ||
}, | ||
"data": { | ||
"sample_name": "sample3", | ||
"profile": { | ||
"sample3": { | ||
"l1": "-", | ||
"l2": "-", | ||
"l3": "26ab0db90d72e28ad0ba1e22ee510510" | ||
} | ||
}, | ||
"seq_data": {} | ||
} | ||
} |
22 changes: 18 additions & 4 deletions
22
tests/data/reports/case-hash-missing/sample3.mlst.subtyping.json
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,7 +1,21 @@ | ||
{ | ||
"sample3": { | ||
"l1": "-", | ||
"l2": "b026324c6904b2a9cb4b88d6d61c81d1", | ||
"l3": "26ab0db90d72e28ad0ba1e22ee510510" | ||
"db_info": {}, | ||
"parameters": { | ||
"mode": "normal", | ||
"min_match_ident": 100, | ||
"min_match_cov": 100, | ||
"max_ambiguous": 0, | ||
"max_internal_stops": 0 | ||
}, | ||
"data": { | ||
"sample_name": "sample3", | ||
"profile": { | ||
"sample3": { | ||
"l1": "-", | ||
"l2": "b026324c6904b2a9cb4b88d6d61c81d1", | ||
"l3": "26ab0db90d72e28ad0ba1e22ee510510" | ||
} | ||
}, | ||
"seq_data": {} | ||
} | ||
} |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,7 +1,21 @@ | ||
{ | ||
"sample1": { | ||
"l1": "1", | ||
"l2": "1", | ||
"l3": "1" | ||
"db_info": {}, | ||
"parameters": { | ||
"mode": "normal", | ||
"min_match_ident": 100, | ||
"min_match_cov": 100, | ||
"max_ambiguous": 0, | ||
"max_internal_stops": 0 | ||
}, | ||
"data": { | ||
"sample_name": "sample1", | ||
"profile": { | ||
"sample1": { | ||
"l1": "1", | ||
"l2": "1", | ||
"l3": "1" | ||
} | ||
}, | ||
"seq_data": {} | ||
} | ||
} |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,7 +1,21 @@ | ||
{ | ||
"sample2": { | ||
"l1": "1", | ||
"l2": "1", | ||
"l3": "1" | ||
"db_info": {}, | ||
"parameters": { | ||
"mode": "normal", | ||
"min_match_ident": 100, | ||
"min_match_cov": 100, | ||
"max_ambiguous": 0, | ||
"max_internal_stops": 0 | ||
}, | ||
"data": { | ||
"sample_name": "sample2", | ||
"profile": { | ||
"sample2": { | ||
"l1": "1", | ||
"l2": "1", | ||
"l3": "1" | ||
} | ||
}, | ||
"seq_data": {} | ||
} | ||
} |
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Could you also add the link to this tag like the other releases, even if the tag isn't created yet (in anticipation of when we release)?
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done here: cf5248e
😃