From becea8d9831d2a3ff2c8a24a8b0ed6015d3718c5 Mon Sep 17 00:00:00 2001 From: kylacochrane Date: Thu, 15 Aug 2024 16:51:54 -0400 Subject: [PATCH 1/9] removed docker tags from container closures --- modules/local/gas/call/main.nf | 2 +- modules/local/locidex/merge/main.nf | 2 +- modules/local/profile_dists/main.nf | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/local/gas/call/main.nf b/modules/local/gas/call/main.nf index 3216c9e..4832e35 100644 --- a/modules/local/gas/call/main.nf +++ b/modules/local/gas/call/main.nf @@ -6,7 +6,7 @@ process GAS_CALL{ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genomic_address_service%3A0.1.1--pyh7cba7a3_1' : - 'quay.io/biocontainers/genomic_address_service:0.1.1--pyh7cba7a3_1' }" + 'biocontainers/genomic_address_service:0.1.1--pyh7cba7a3_1' }" input: diff --git a/modules/local/locidex/merge/main.nf b/modules/local/locidex/merge/main.nf index 7721625..226ba1f 100644 --- a/modules/local/locidex/merge/main.nf +++ b/modules/local/locidex/merge/main.nf @@ -6,7 +6,7 @@ process LOCIDEX_MERGE { container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/locidex:0.1.1--pyhdfd78af_0' : - 'quay.io/biocontainers/locidex:0.1.1--pyhdfd78af_0' }" + 'biocontainers/locidex:0.1.1--pyhdfd78af_0' }" input: path input_values // [file(sample1), file(sample2), file(sample3), etc...] diff --git a/modules/local/profile_dists/main.nf b/modules/local/profile_dists/main.nf index f43d63b..b6b92de 100644 --- a/modules/local/profile_dists/main.nf +++ b/modules/local/profile_dists/main.nf @@ -4,7 +4,7 @@ process PROFILE_DISTS{ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/profile_dists%3A1.0.0--pyh7cba7a3_0' : - 'quay.io/biocontainers/profile_dists:1.0.0--pyh7cba7a3_0' }" + 'biocontainers/profile_dists:1.0.0--pyh7cba7a3_0' }" input: path query From 5dfde61db4d31a00ead7c318a46c10861ca4bd95 Mon Sep 17 00:00:00 2001 From: kylacochrane Date: Fri, 16 Aug 2024 10:57:51 -0400 Subject: [PATCH 2/9] Updated CHANGELOG.md --- CHANGELOG.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4b7a138..89b82db 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## Unreleased + +### `Changed` + +- Removed `quay.io` docker repository tags from modules [PR19](https://github.com/phac-nml/gasnomenclature/pull/19) + ## [0.1.0] - 2024/06/28 Initial release of the Genomic Address Nomenclature pipeline to be used to assign cluster addresses to samples based on an existing cluster designations. From 350809638d02b511de189323467407e8dd5cd6ad Mon Sep 17 00:00:00 2001 From: kylacochrane Date: Thu, 22 Aug 2024 14:47:17 -0400 Subject: [PATCH 3/9] Revised mlst.json reports in tests/data to meet the formatting requirements of locidex 0.2.3. --- tests/data/reports/sample1.mlst.json | 22 ++++++++++--- tests/data/reports/sample1.mlst.json.gz | Bin 84 -> 207 bytes tests/data/reports/sample2.mlst.json | 22 ++++++++++--- tests/data/reports/sample2_missing.mlst.json | 22 ++++++++++--- tests/data/reports/sample3.mlst.json | 22 ++++++++++--- tests/data/reports/sample3_missing.mlst.json | 22 ++++++++++--- .../reports/sample3_multiplekeys.mlst.json | 30 +++++++++++++----- .../sample3_multiplekeys_nomatch.mlst.json | 30 +++++++++++++----- tests/data/reports/sample7.mlst.json | 22 ++++++++++--- tests/data/reports/sampleF.mlst.json | 22 ++++++++++--- tests/data/reports/sampleN.mlst.json | 22 ++++++++++--- tests/data/reports/sampleQ.mlst.json | 22 ++++++++++--- 12 files changed, 206 insertions(+), 52 deletions(-) diff --git a/tests/data/reports/sample1.mlst.json b/tests/data/reports/sample1.mlst.json index 01bc774..63a71b4 100644 --- a/tests/data/reports/sample1.mlst.json +++ b/tests/data/reports/sample1.mlst.json @@ -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": {} } } diff --git a/tests/data/reports/sample1.mlst.json.gz b/tests/data/reports/sample1.mlst.json.gz index 735e1082b5193673c4844e4f4558af8e8206a12f..512cf985d783b0ac8e0644fa71156f17d6baba20 100644 GIT binary patch literal 207 zcmV;=05Ja_iwFoTg2!e619M?*aBO8UE^TacbS`RhZ*Bl}kIN3iAP`0O{fdTl7p?C6 z88R(XCE+DdW76>N@<^3hWjFWCFlW}LjgPRAay4smY1hz|$bbcj9<57h&T=j_!s~UXgrDIn=_&>X{4Nja8$=0c0prPU??7==2|*3)+$Ju0o~d@J_dLN=Ily^8zT! Jy#uNN007@EUpN2& literal 84 zcmb2|=HNKSm6gWyzc?|sAScyOFE^*SL@%p2KaXM6vmgehrH_u>X_^z_tg79bwSghR ofc;3gQOG4nA)`YgMr|C8u30;?7#SEC{{LrYxbRPWOAwF^07ax8@c;k- diff --git a/tests/data/reports/sample2.mlst.json b/tests/data/reports/sample2.mlst.json index 7c0426c..3d9ee23 100644 --- a/tests/data/reports/sample2.mlst.json +++ b/tests/data/reports/sample2.mlst.json @@ -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": {} } } diff --git a/tests/data/reports/sample2_missing.mlst.json b/tests/data/reports/sample2_missing.mlst.json index 113e15b..58c2d70 100644 --- a/tests/data/reports/sample2_missing.mlst.json +++ b/tests/data/reports/sample2_missing.mlst.json @@ -1,7 +1,21 @@ { - "sample2": { - "l1": "-", - "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": "-", + "l2": "1", + "l3": "1" + } + }, + "seq_data": {} } } diff --git a/tests/data/reports/sample3.mlst.json b/tests/data/reports/sample3.mlst.json index 43ea3c7..d57ee75 100644 --- a/tests/data/reports/sample3.mlst.json +++ b/tests/data/reports/sample3.mlst.json @@ -1,7 +1,21 @@ { - "sample3": { - "l1": "1", - "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": "1", + "l2": "1", + "l3": "2" + } + }, + "seq_data": {} } } diff --git a/tests/data/reports/sample3_missing.mlst.json b/tests/data/reports/sample3_missing.mlst.json index 49942f8..ac6eab5 100644 --- a/tests/data/reports/sample3_missing.mlst.json +++ b/tests/data/reports/sample3_missing.mlst.json @@ -1,7 +1,21 @@ { - "sample3": { - "l1": "-", - "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": "-", + "l2": "1", + "l3": "2" + } + }, + "seq_data": {} } } diff --git a/tests/data/reports/sample3_multiplekeys.mlst.json b/tests/data/reports/sample3_multiplekeys.mlst.json index 5d85e65..8b1fc52 100644 --- a/tests/data/reports/sample3_multiplekeys.mlst.json +++ b/tests/data/reports/sample3_multiplekeys.mlst.json @@ -1,12 +1,26 @@ { - "extra_key": { - "l1": "1", - "l2": "1", - "l3": "2" + "db_info": {}, + "parameters": { + "mode": "normal", + "min_match_ident": 100, + "min_match_cov": 100, + "max_ambiguous": 0, + "max_internal_stops": 0 }, - "sample3": { - "l1": "1", - "l2": "1", - "l3": "2" + "data": { + "sample_name": "sample3", + "profile": { + "extra_key": { + "l1": "1", + "l2": "1", + "l3": "2" + }, + "sample3": { + "l1": "1", + "l2": "1", + "l3": "2" + } + }, + "seq_data": {} } } diff --git a/tests/data/reports/sample3_multiplekeys_nomatch.mlst.json b/tests/data/reports/sample3_multiplekeys_nomatch.mlst.json index 6d7878d..42f8bd8 100644 --- a/tests/data/reports/sample3_multiplekeys_nomatch.mlst.json +++ b/tests/data/reports/sample3_multiplekeys_nomatch.mlst.json @@ -1,12 +1,26 @@ { - "sample4": { - "l1": "1", - "l2": "1", - "l3": "2" + "db_info": {}, + "parameters": { + "mode": "normal", + "min_match_ident": 100, + "min_match_cov": 100, + "max_ambiguous": 0, + "max_internal_stops": 0 }, - "extra_key": { - "l1": "1", - "l2": "1", - "l3": "2" + "data": { + "sample_name": "sample4", + "profile": { + "sample4": { + "l1": "1", + "l2": "1", + "l3": "2" + }, + "extra_key": { + "l1": "1", + "l2": "1", + "l3": "2" + } + }, + "seq_data": {} } } diff --git a/tests/data/reports/sample7.mlst.json b/tests/data/reports/sample7.mlst.json index 41d6312..2e33871 100644 --- a/tests/data/reports/sample7.mlst.json +++ b/tests/data/reports/sample7.mlst.json @@ -1,7 +1,21 @@ { - "sample7": { - "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": "sample7", + "profile": { + "sample7": { + "l1": "1", + "l2": "1", + "l3": "1" + } + }, + "seq_data": {} } } diff --git a/tests/data/reports/sampleF.mlst.json b/tests/data/reports/sampleF.mlst.json index 8c09d39..4792244 100644 --- a/tests/data/reports/sampleF.mlst.json +++ b/tests/data/reports/sampleF.mlst.json @@ -1,7 +1,21 @@ { - "sampleF": { - "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": "sampleF", + "profile": { + "sampleF": { + "l1": "1", + "l2": "2", + "l3": "1" + } + }, + "seq_data": {} } } diff --git a/tests/data/reports/sampleN.mlst.json b/tests/data/reports/sampleN.mlst.json index 178b6db..fd60cec 100644 --- a/tests/data/reports/sampleN.mlst.json +++ b/tests/data/reports/sampleN.mlst.json @@ -1,7 +1,21 @@ { - "sampleN": { - "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": "sampleN", + "profile": { + "sampleN": { + "l1": "1", + "l2": "2", + "l3": "1" + } + }, + "seq_data": {} } } diff --git a/tests/data/reports/sampleQ.mlst.json b/tests/data/reports/sampleQ.mlst.json index c6cca43..a8f60ba 100644 --- a/tests/data/reports/sampleQ.mlst.json +++ b/tests/data/reports/sampleQ.mlst.json @@ -1,7 +1,21 @@ { - "sampleQ": { - "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": "sampleQ", + "profile": { + "sampleQ": { + "l1": "1", + "l2": "2", + "l3": "1" + } + }, + "seq_data": {} } } From b498fdd2c35c2772be7e21c8f108aa452395b05b Mon Sep 17 00:00:00 2001 From: kylacochrane Date: Fri, 23 Aug 2024 09:41:27 -0400 Subject: [PATCH 4/9] Update to locidex:0.2.3 and alter input_assure.py to comply with mlst.json format --- assets/samplesheet.csv | 8 ++++---- bin/input_assure.py | 27 ++++++++++++++++----------- modules/local/locidex/merge/main.nf | 5 +++-- nextflow.config | 3 +++ 4 files changed, 26 insertions(+), 17 deletions(-) diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index b0d6f9e..72c50a7 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -1,5 +1,5 @@ sample,mlst_alleles,address -sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json, -sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1.1.1 -sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2.mlst.json,1.1.1 -sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3.mlst.json,1.1.2 +sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleQ.mlst.json, +sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample1.mlst.json,1.1.1 +sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample2.mlst.json,1.1.1 +sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample3.mlst.json,1.1.2 diff --git a/bin/input_assure.py b/bin/input_assure.py index d99bf2a..e2b7ac1 100755 --- a/bin/input_assure.py +++ b/bin/input_assure.py @@ -19,18 +19,22 @@ def check_inputs(json_file, sample_id, address, output_error_file, output_json_f with open_file(json_file, "rt") as f: json_data = json.load(f) + # Extract the profile from the json_data + profile = json_data.get("data", {}).get("profile", {}) + # Check for multiple keys in the JSON file and define error message + keys = sorted(profile.keys()) + original_key = keys[0] if keys else None + # Define a variable to store the match_status (True or False) - match_status = sample_id in json_data + match_status = sample_id in profile # Initialize the error message error_message = None - # Check for multiple keys in the JSON file and define error message - keys = list(json_data.keys()) - original_key = keys[0] if keys else None - - if len(keys) == 0: - error_message = f"{json_file} is completely empty!" + if not keys: + error_message = ( + f"{json_file} is missing the 'profile' section or is completely empty!" + ) print(error_message) sys.exit(1) elif len(keys) > 1: @@ -38,11 +42,11 @@ def check_inputs(json_file, sample_id, address, output_error_file, output_json_f if not match_status: error_message = f"No key in the MLST JSON file ({json_file}) matches the specified sample ID '{sample_id}'. The first key '{original_key}' has been forcefully changed to '{sample_id}' and all other keys have been removed." # Retain only the specified sample ID - json_data = {sample_id: json_data.pop(original_key)} + json_data["data"]["profile"] = {sample_id: profile.pop(original_key)} else: error_message = f"MLST JSON file ({json_file}) contains multiple keys: {keys}. The MLST JSON file has been modified to retain only the '{sample_id}' entry" - # Remove all keys expect the one matching sample_id - json_data = {sample_id: json_data[sample_id]} + # Retain only the specified sample_id in the profile + json_data["data"]["profile"] = {sample_id: profile[sample_id]} elif not match_status: # Define error message based on meta.address (query or reference) if address == "null": @@ -50,7 +54,8 @@ def check_inputs(json_file, sample_id, address, output_error_file, output_json_f else: error_message = f"Reference {sample_id} ID and JSON key in {json_file} DO NOT MATCH. The '{original_key}' key in {json_file} has been forcefully changed to '{sample_id}': User should manually check input files to ensure correctness." # Update the JSON file with the new sample ID - json_data[sample_id] = json_data.pop(original_key) + json_data["data"]["profile"] = {sample_id: profile.pop(original_key)} + json_data["data"]["sample_name"] = sample_id # Write file containing relevant error messages if error_message: diff --git a/modules/local/locidex/merge/main.nf b/modules/local/locidex/merge/main.nf index 226ba1f..170cb88 100644 --- a/modules/local/locidex/merge/main.nf +++ b/modules/local/locidex/merge/main.nf @@ -5,8 +5,9 @@ process LOCIDEX_MERGE { label 'process_medium' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/locidex:0.1.1--pyhdfd78af_0' : - 'biocontainers/locidex:0.1.1--pyhdfd78af_0' }" + "docker.io/mwells14/locidex:0.2.3" : + task.ext.override_configured_container_registry != false ? 'docker.io/mwells14/locidex:0.2.3' : + 'mwells14/locidex:0.2.3' }" input: path input_values // [file(sample1), file(sample2), file(sample3), etc...] diff --git a/nextflow.config b/nextflow.config index 423d59c..b651d04 100644 --- a/nextflow.config +++ b/nextflow.config @@ -168,6 +168,9 @@ 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 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet From 818ccecd144fbe7330f6982b9f84079547a68c5c Mon Sep 17 00:00:00 2001 From: kylacochrane Date: Fri, 23 Aug 2024 09:43:18 -0400 Subject: [PATCH 5/9] Update main.nf.test expected outcomes and update test samplesheets --- tests/data/samplesheets/samplesheet-hash_missing.csv | 8 ++++---- tests/data/samplesheets/samplesheet-mismatched_IDs.csv | 10 +++++----- tests/data/samplesheets/samplesheet-multiple_keys.csv | 8 ++++---- .../data/samplesheets/samplesheet-multiple_queries.csv | 10 +++++----- .../samplesheets/samplesheet-multiplekeys_nomatch.csv | 8 ++++---- tests/data/samplesheets/samplesheet1.csv | 8 ++++---- tests/data/samplesheets/samplesheet_emptyJSON.csv | 8 ++++---- tests/data/samplesheets/samplesheet_gzip.csv | 8 ++++---- tests/data/samplesheets/samplesheet_thresh_1.csv | 8 ++++---- tests/data/samplesheets/samplesheet_thresh_1_0.csv | 8 ++++---- tests/pipelines/main.nf.test | 4 ++-- 11 files changed, 44 insertions(+), 44 deletions(-) diff --git a/tests/data/samplesheets/samplesheet-hash_missing.csv b/tests/data/samplesheets/samplesheet-hash_missing.csv index 7bfe7af..cc1b61f 100644 --- a/tests/data/samplesheets/samplesheet-hash_missing.csv +++ b/tests/data/samplesheets/samplesheet-hash_missing.csv @@ -1,5 +1,5 @@ sample,mlst_alleles,address -sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json, -sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1 -sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2_missing.mlst.json,1 -sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3_missing.mlst.json,2 +sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleQ.mlst.json, +sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample1.mlst.json,1 +sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample2_missing.mlst.json,1 +sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample3_missing.mlst.json,2 diff --git a/tests/data/samplesheets/samplesheet-mismatched_IDs.csv b/tests/data/samplesheets/samplesheet-mismatched_IDs.csv index 73230d4..68231ef 100644 --- a/tests/data/samplesheets/samplesheet-mismatched_IDs.csv +++ b/tests/data/samplesheets/samplesheet-mismatched_IDs.csv @@ -1,7 +1,7 @@ sample,mlst_alleles,address -sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json, -sampleR,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleF.mlst.json, -sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1.1.1 -sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample7.mlst.json,1.1.1 -sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3.mlst.json,1.1.2 +sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleQ.mlst.json, +sampleR,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleF.mlst.json, +sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample1.mlst.json,1.1.1 +sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample7.mlst.json,1.1.1 +sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample3.mlst.json,1.1.2 diff --git a/tests/data/samplesheets/samplesheet-multiple_keys.csv b/tests/data/samplesheets/samplesheet-multiple_keys.csv index 74f034a..7263ee3 100644 --- a/tests/data/samplesheets/samplesheet-multiple_keys.csv +++ b/tests/data/samplesheets/samplesheet-multiple_keys.csv @@ -1,5 +1,5 @@ sample,mlst_alleles,address -sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json, -sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1.1.1 -sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2.mlst.json,1.1.1 -sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3_multiplekeys.mlst.json,1.1.2 +sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleQ.mlst.json, +sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample1.mlst.json,1.1.1 +sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample2.mlst.json,1.1.1 +sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample3_multiplekeys.mlst.json,1.1.2 diff --git a/tests/data/samplesheets/samplesheet-multiple_queries.csv b/tests/data/samplesheets/samplesheet-multiple_queries.csv index c8e76de..e7c6af8 100644 --- a/tests/data/samplesheets/samplesheet-multiple_queries.csv +++ b/tests/data/samplesheets/samplesheet-multiple_queries.csv @@ -1,6 +1,6 @@ sample,mlst_alleles,address -sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json, -sampleN,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleN.mlst.json, -sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1.1.1 -sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2.mlst.json,1.1.1 -sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3.mlst.json,1.1.2 +sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleQ.mlst.json, +sampleN,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleN.mlst.json, +sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample1.mlst.json,1.1.1 +sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample2.mlst.json,1.1.1 +sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample3.mlst.json,1.1.2 diff --git a/tests/data/samplesheets/samplesheet-multiplekeys_nomatch.csv b/tests/data/samplesheets/samplesheet-multiplekeys_nomatch.csv index 90d6289..2e8bd2b 100644 --- a/tests/data/samplesheets/samplesheet-multiplekeys_nomatch.csv +++ b/tests/data/samplesheets/samplesheet-multiplekeys_nomatch.csv @@ -1,5 +1,5 @@ sample,mlst_alleles,address -sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json, -sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1.1.1 -sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2.mlst.json,1.1.1 -sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3_multiplekeys_nomatch.mlst.json,1.1.2 +sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleQ.mlst.json, +sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample1.mlst.json,1.1.1 +sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample2.mlst.json,1.1.1 +sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample3_multiplekeys_nomatch.mlst.json,1.1.2 diff --git a/tests/data/samplesheets/samplesheet1.csv b/tests/data/samplesheets/samplesheet1.csv index b0d6f9e..72c50a7 100644 --- a/tests/data/samplesheets/samplesheet1.csv +++ b/tests/data/samplesheets/samplesheet1.csv @@ -1,5 +1,5 @@ sample,mlst_alleles,address -sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json, -sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1.1.1 -sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2.mlst.json,1.1.1 -sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3.mlst.json,1.1.2 +sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleQ.mlst.json, +sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample1.mlst.json,1.1.1 +sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample2.mlst.json,1.1.1 +sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample3.mlst.json,1.1.2 diff --git a/tests/data/samplesheets/samplesheet_emptyJSON.csv b/tests/data/samplesheets/samplesheet_emptyJSON.csv index 0b84688..dc349ff 100644 --- a/tests/data/samplesheets/samplesheet_emptyJSON.csv +++ b/tests/data/samplesheets/samplesheet_emptyJSON.csv @@ -1,6 +1,6 @@ sample,mlst_alleles,address -sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json, -sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1.1.1 -sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2_empty.mlst.json,1.1.1 -sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3.mlst.json,1.1.2 +sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleQ.mlst.json, +sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample1.mlst.json,1.1.1 +sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample2_empty.mlst.json,1.1.1 +sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample3.mlst.json,1.1.2 diff --git a/tests/data/samplesheets/samplesheet_gzip.csv b/tests/data/samplesheets/samplesheet_gzip.csv index e35b3e9..1f467a1 100644 --- a/tests/data/samplesheets/samplesheet_gzip.csv +++ b/tests/data/samplesheets/samplesheet_gzip.csv @@ -1,5 +1,5 @@ sample,mlst_alleles,address -sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json, -sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json.gz,1.1.1 -sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2.mlst.json,1.1.1 -sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3.mlst.json,1.1.2 +sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleQ.mlst.json, +sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample1.mlst.json.gz,1.1.1 +sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample2.mlst.json,1.1.1 +sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample3.mlst.json,1.1.2 diff --git a/tests/data/samplesheets/samplesheet_thresh_1.csv b/tests/data/samplesheets/samplesheet_thresh_1.csv index f4b6b93..6e1ae15 100644 --- a/tests/data/samplesheets/samplesheet_thresh_1.csv +++ b/tests/data/samplesheets/samplesheet_thresh_1.csv @@ -1,5 +1,5 @@ sample,mlst_alleles,address -sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json, -sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1 -sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2.mlst.json,1 -sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3.mlst.json,1 +sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleQ.mlst.json, +sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample1.mlst.json,1 +sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample2.mlst.json,1 +sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample3.mlst.json,1 diff --git a/tests/data/samplesheets/samplesheet_thresh_1_0.csv b/tests/data/samplesheets/samplesheet_thresh_1_0.csv index 9260f3f..c7e7224 100644 --- a/tests/data/samplesheets/samplesheet_thresh_1_0.csv +++ b/tests/data/samplesheets/samplesheet_thresh_1_0.csv @@ -1,5 +1,5 @@ sample,mlst_alleles,address -sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json, -sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1.1 -sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2.mlst.json,1.1 -sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3.mlst.json,1.1 +sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleQ.mlst.json, +sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample1.mlst.json,1.1 +sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample2.mlst.json,1.1 +sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample3.mlst.json,1.1 diff --git a/tests/pipelines/main.nf.test b/tests/pipelines/main.nf.test index 223b7de..97a935e 100644 --- a/tests/pipelines/main.nf.test +++ b/tests/pipelines/main.nf.test @@ -317,7 +317,7 @@ nextflow_pipeline { // Ensure that the error_reports are generated for query and reference samples lines = path("$launchDir/results/input/sample3_error_report.csv").readLines() - assert lines.contains("sample3,\"[\'sample4\', \'extra_key\']\",No key in the MLST JSON file (sample3_multiplekeys_nomatch.mlst.json) matches the specified sample ID \'sample3\'. The first key \'sample4\' has been forcefully changed to \'sample3\' and all other keys have been removed.") + assert lines.contains('sample3,"[\'extra_key\', \'sample4\']",No key in the MLST JSON file (sample3_multiplekeys_nomatch.mlst.json) matches the specified sample ID \'sample3\'. The first key \'extra_key\' has been forcefully changed to \'sample3\' and all other keys have been removed.') // Check filtered query csv results lines = path("$launchDir/results/filter/new_addresses.csv").readLines() @@ -351,7 +351,7 @@ nextflow_pipeline { then { assert workflow.failed - assert (workflow.stdout =~ /sample2_empty.mlst.json is completely empty!/).find() + assert (workflow.stdout =~ /sample2_empty.mlst.json is missing the 'profile' section or is completely empty!/).find() } } } From 1b9b1edfc17ca8cb75b0aa85b7d95beffbf2e2b3 Mon Sep 17 00:00:00 2001 From: kylacochrane Date: Fri, 23 Aug 2024 09:53:52 -0400 Subject: [PATCH 6/9] Updated CHANGELOG.md and nextflow.config manifest version --- CHANGELOG.md | 4 +++- nextflow.config | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 89b82db..3945297 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,10 +3,11 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## Unreleased +## [0.2.0] - 2024/08/23 ### `Changed` +- Upgraded `locidex/merge` to version `0.2.3` and updated `input_assure.py` and test data for compatibility with the new `mlst.json` allele file format [PR20](https://github.com/phac-nml/gasnomenclature/pull/20) - Removed `quay.io` docker repository tags from modules [PR19](https://github.com/phac-nml/gasnomenclature/pull/19) ## [0.1.0] - 2024/06/28 @@ -19,3 +20,4 @@ Initial release of the Genomic Address Nomenclature pipeline to be used to assig - Output of assigned cluster addresses for any **query** samples using [profile_dists](https://github.com/phac-nml/profile_dists) and [gas call](https://github.com/phac-nml/genomic_address_service). [0.1.0]: https://github.com/phac-nml/gasnomenclature/releases/tag/0.1.0 +[0.2.0]: https://github.com/phac-nml/gasnomenclature/releases/tag/0.2.0 diff --git a/nextflow.config b/nextflow.config index b651d04..1882e6f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -222,7 +222,7 @@ manifest { description = """Gas Nomenclature assignment pipeline""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '0.1.0' + version = '0.2.0' doi = '' defaultBranch = 'main' } From 01f3309e9b64ad8ad13a1805cdb6a70d613c8b47 Mon Sep 17 00:00:00 2001 From: kylacochrane Date: Thu, 5 Sep 2024 10:22:28 -0400 Subject: [PATCH 7/9] Updated CHANGELOG --- CHANGELOG.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3945297..67ef724 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,13 +3,15 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [0.2.0] - 2024/08/23 +## [0.2.0] - 2024/09/05 ### `Changed` - Upgraded `locidex/merge` to version `0.2.3` and updated `input_assure.py` and test data for compatibility with the new `mlst.json` allele file format [PR20](https://github.com/phac-nml/gasnomenclature/pull/20) - Removed `quay.io` docker repository tags from modules [PR19](https://github.com/phac-nml/gasnomenclature/pull/19) +This pipeline is now compatible only with output generated by [Locidex v0.2.3+](https://github.com/phac-nml/locidex) and [Mikrokondo v0.4.0+](https://github.com/phac-nml/mikrokondo/releases/tag/v0.4.0). + ## [0.1.0] - 2024/06/28 Initial release of the Genomic Address Nomenclature pipeline to be used to assign cluster addresses to samples based on an existing cluster designations. From a5836e6833d2b54cfda5246ffb371ea76ba1e32b Mon Sep 17 00:00:00 2001 From: kylacochrane Date: Thu, 5 Sep 2024 10:22:57 -0400 Subject: [PATCH 8/9] Updated test data file paths --- tests/data/samplesheets/samplesheet-hash_missing.csv | 8 ++++---- tests/data/samplesheets/samplesheet-mismatched_IDs.csv | 10 +++++----- tests/data/samplesheets/samplesheet-multiple_keys.csv | 8 ++++---- .../data/samplesheets/samplesheet-multiple_queries.csv | 10 +++++----- .../samplesheets/samplesheet-multiplekeys_nomatch.csv | 8 ++++---- tests/data/samplesheets/samplesheet1.csv | 8 ++++---- tests/data/samplesheets/samplesheet_emptyJSON.csv | 8 ++++---- tests/data/samplesheets/samplesheet_gzip.csv | 8 ++++---- tests/data/samplesheets/samplesheet_thresh_1.csv | 8 ++++---- tests/data/samplesheets/samplesheet_thresh_1_0.csv | 8 ++++---- 10 files changed, 42 insertions(+), 42 deletions(-) diff --git a/tests/data/samplesheets/samplesheet-hash_missing.csv b/tests/data/samplesheets/samplesheet-hash_missing.csv index cc1b61f..7bfe7af 100644 --- a/tests/data/samplesheets/samplesheet-hash_missing.csv +++ b/tests/data/samplesheets/samplesheet-hash_missing.csv @@ -1,5 +1,5 @@ sample,mlst_alleles,address -sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleQ.mlst.json, -sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample1.mlst.json,1 -sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample2_missing.mlst.json,1 -sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample3_missing.mlst.json,2 +sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json, +sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1 +sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2_missing.mlst.json,1 +sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3_missing.mlst.json,2 diff --git a/tests/data/samplesheets/samplesheet-mismatched_IDs.csv b/tests/data/samplesheets/samplesheet-mismatched_IDs.csv index 68231ef..73230d4 100644 --- a/tests/data/samplesheets/samplesheet-mismatched_IDs.csv +++ b/tests/data/samplesheets/samplesheet-mismatched_IDs.csv @@ -1,7 +1,7 @@ sample,mlst_alleles,address -sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleQ.mlst.json, -sampleR,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleF.mlst.json, -sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample1.mlst.json,1.1.1 -sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample7.mlst.json,1.1.1 -sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample3.mlst.json,1.1.2 +sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json, +sampleR,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleF.mlst.json, +sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1.1.1 +sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample7.mlst.json,1.1.1 +sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3.mlst.json,1.1.2 diff --git a/tests/data/samplesheets/samplesheet-multiple_keys.csv b/tests/data/samplesheets/samplesheet-multiple_keys.csv index 7263ee3..74f034a 100644 --- a/tests/data/samplesheets/samplesheet-multiple_keys.csv +++ b/tests/data/samplesheets/samplesheet-multiple_keys.csv @@ -1,5 +1,5 @@ sample,mlst_alleles,address -sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleQ.mlst.json, -sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample1.mlst.json,1.1.1 -sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample2.mlst.json,1.1.1 -sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample3_multiplekeys.mlst.json,1.1.2 +sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json, +sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1.1.1 +sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2.mlst.json,1.1.1 +sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3_multiplekeys.mlst.json,1.1.2 diff --git a/tests/data/samplesheets/samplesheet-multiple_queries.csv b/tests/data/samplesheets/samplesheet-multiple_queries.csv index e7c6af8..c8e76de 100644 --- a/tests/data/samplesheets/samplesheet-multiple_queries.csv +++ b/tests/data/samplesheets/samplesheet-multiple_queries.csv @@ -1,6 +1,6 @@ sample,mlst_alleles,address -sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleQ.mlst.json, -sampleN,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleN.mlst.json, -sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample1.mlst.json,1.1.1 -sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample2.mlst.json,1.1.1 -sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample3.mlst.json,1.1.2 +sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json, +sampleN,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleN.mlst.json, +sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1.1.1 +sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2.mlst.json,1.1.1 +sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3.mlst.json,1.1.2 diff --git a/tests/data/samplesheets/samplesheet-multiplekeys_nomatch.csv b/tests/data/samplesheets/samplesheet-multiplekeys_nomatch.csv index 2e8bd2b..90d6289 100644 --- a/tests/data/samplesheets/samplesheet-multiplekeys_nomatch.csv +++ b/tests/data/samplesheets/samplesheet-multiplekeys_nomatch.csv @@ -1,5 +1,5 @@ sample,mlst_alleles,address -sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleQ.mlst.json, -sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample1.mlst.json,1.1.1 -sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample2.mlst.json,1.1.1 -sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample3_multiplekeys_nomatch.mlst.json,1.1.2 +sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json, +sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1.1.1 +sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2.mlst.json,1.1.1 +sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3_multiplekeys_nomatch.mlst.json,1.1.2 diff --git a/tests/data/samplesheets/samplesheet1.csv b/tests/data/samplesheets/samplesheet1.csv index 72c50a7..b0d6f9e 100644 --- a/tests/data/samplesheets/samplesheet1.csv +++ b/tests/data/samplesheets/samplesheet1.csv @@ -1,5 +1,5 @@ sample,mlst_alleles,address -sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleQ.mlst.json, -sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample1.mlst.json,1.1.1 -sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample2.mlst.json,1.1.1 -sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample3.mlst.json,1.1.2 +sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json, +sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1.1.1 +sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2.mlst.json,1.1.1 +sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3.mlst.json,1.1.2 diff --git a/tests/data/samplesheets/samplesheet_emptyJSON.csv b/tests/data/samplesheets/samplesheet_emptyJSON.csv index dc349ff..0b84688 100644 --- a/tests/data/samplesheets/samplesheet_emptyJSON.csv +++ b/tests/data/samplesheets/samplesheet_emptyJSON.csv @@ -1,6 +1,6 @@ sample,mlst_alleles,address -sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleQ.mlst.json, -sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample1.mlst.json,1.1.1 -sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample2_empty.mlst.json,1.1.1 -sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample3.mlst.json,1.1.2 +sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json, +sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1.1.1 +sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2_empty.mlst.json,1.1.1 +sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3.mlst.json,1.1.2 diff --git a/tests/data/samplesheets/samplesheet_gzip.csv b/tests/data/samplesheets/samplesheet_gzip.csv index 1f467a1..e35b3e9 100644 --- a/tests/data/samplesheets/samplesheet_gzip.csv +++ b/tests/data/samplesheets/samplesheet_gzip.csv @@ -1,5 +1,5 @@ sample,mlst_alleles,address -sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleQ.mlst.json, -sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample1.mlst.json.gz,1.1.1 -sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample2.mlst.json,1.1.1 -sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample3.mlst.json,1.1.2 +sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json, +sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json.gz,1.1.1 +sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2.mlst.json,1.1.1 +sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3.mlst.json,1.1.2 diff --git a/tests/data/samplesheets/samplesheet_thresh_1.csv b/tests/data/samplesheets/samplesheet_thresh_1.csv index 6e1ae15..f4b6b93 100644 --- a/tests/data/samplesheets/samplesheet_thresh_1.csv +++ b/tests/data/samplesheets/samplesheet_thresh_1.csv @@ -1,5 +1,5 @@ sample,mlst_alleles,address -sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleQ.mlst.json, -sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample1.mlst.json,1 -sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample2.mlst.json,1 -sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample3.mlst.json,1 +sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json, +sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1 +sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2.mlst.json,1 +sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3.mlst.json,1 diff --git a/tests/data/samplesheets/samplesheet_thresh_1_0.csv b/tests/data/samplesheets/samplesheet_thresh_1_0.csv index c7e7224..9260f3f 100644 --- a/tests/data/samplesheets/samplesheet_thresh_1_0.csv +++ b/tests/data/samplesheets/samplesheet_thresh_1_0.csv @@ -1,5 +1,5 @@ sample,mlst_alleles,address -sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleQ.mlst.json, -sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample1.mlst.json,1.1 -sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample2.mlst.json,1.1 -sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample3.mlst.json,1.1 +sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json, +sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1.1 +sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2.mlst.json,1.1 +sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3.mlst.json,1.1 From 03b0d3a4a2257ec32dbaf69ab4588bf4fe9c3c2d Mon Sep 17 00:00:00 2001 From: kylacochrane Date: Thu, 5 Sep 2024 12:54:30 -0400 Subject: [PATCH 9/9] Update file path to test data in assets/samplesheet.csv --- assets/samplesheet.csv | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index 72c50a7..b0d6f9e 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -1,5 +1,5 @@ sample,mlst_alleles,address -sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sampleQ.mlst.json, -sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample1.mlst.json,1.1.1 -sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample2.mlst.json,1.1.1 -sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/update/input_assure/tests/data/reports/sample3.mlst.json,1.1.2 +sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json, +sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1.1.1 +sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2.mlst.json,1.1.1 +sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3.mlst.json,1.1.2