ci: drop pytest in favor of Sprocket test #263
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@@ -7,6 +7,3 @@ jobs: | |
| call-build: | ||
| uses: ./.github/workflows/docker-build.yaml | ||
| secrets: inherit | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,4 @@ | ||
| pytest/ | ||
| # Ignore common bioinformatics formats used in these workflows. | ||
| # But only if they are in the root of this repo | ||
| /*.fastq.gz | ||
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@@ -106,7 +106,7 @@ task validate_string_is_12bit_int { | |
| >>> | ||
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| runtime { | ||
| container: "ghcr.io/stjudecloud/util:branch-sprocket-test-3.0.4" | ||
| maxRetries: 1 | ||
| } | ||
| } | ||
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@@ -82,7 +82,9 @@ workflow read_group_to_string { | |
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| input { | ||
| ReadGroup read_group | ||
| Array[String] required_fields = [ | ||
| "SM", | ||
| ] | ||
| Boolean format_as_sam_record = false | ||
| Boolean restrictive = true | ||
| } | ||
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@@ -136,7 +138,7 @@ task get_read_groups { | |
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| runtime { | ||
| disks: "~{disk_size_gb} GB" | ||
| container: "ghcr.io/stjudecloud/util:branch-sprocket-test-3.0.4" | ||
| maxRetries: 1 | ||
| } | ||
| } | ||
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@@ -147,22 +149,20 @@ task validate_read_group { | |
| } | ||
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| parameter_meta { | ||
| required_fields: "Array of read group fields that must be defined. The ID field is always required and does not need to be specified." | ||
| read_group: "`ReadGroup` struct to validate" | ||
| restrictive: "If true, run a stricter validation of field values. Otherwise, check against SAM spec-defined values." | ||
| } | ||
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| input { | ||
| Array[String] required_fields | ||
| ReadGroup read_group | ||
| Boolean restrictive | ||
| } | ||
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| # The SAM spec allows any printable ASCII character in header fields. | ||
| String sam_spec_pattern = "[\\ -~]+" | ||
| # We have the opinion that is too permissive for ID and SM. | ||
| String restrictive_pattern = "\\ " # Disallow spaces | ||
| Array[String] platforms = [ | ||
| "CAPILLARY", | ||
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@@ -182,11 +182,9 @@ task validate_read_group { | |
| command <<< | ||
| exit_code=0 | ||
| if ~{restrictive}; then | ||
| if [[ "~{read_group.ID}" =~ ~{restrictive_pattern} ]] | ||
| then | ||
| >&2 echo "ID must not contain spaces" | ||
| exit_code=1 | ||
| fi | ||
| fi | ||
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@@ -202,11 +200,9 @@ task validate_read_group { | |
| fi | ||
| if ~{defined(read_group.SM)}; then | ||
| if ~{restrictive}; then | ||
| if [[ "~{read_group.SM}" =~ ~{restrictive_pattern} ]] | ||
| then | ||
| >&2 echo "SM must not contain spaces" | ||
| exit_code=1 | ||
| fi | ||
| fi | ||
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@@ -367,7 +363,7 @@ task validate_read_group { | |
| >>> | ||
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| runtime { | ||
| container: "ghcr.io/stjudecloud/util:branch-sprocket-test-3.0.4" | ||
| maxRetries: 1 | ||
| } | ||
| } | ||
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@@ -391,7 +387,7 @@ task inner_read_group_to_string { | |
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| input { | ||
| ReadGroup read_group | ||
| Boolean format_as_sam_record | ||
| } | ||
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| String delimiter = if format_as_sam_record | ||
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@@ -425,7 +421,7 @@ task inner_read_group_to_string { | |
| } | ||
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| runtime { | ||
| container: "ghcr.io/stjudecloud/util:branch-sprocket-test-3.0.4" | ||
| maxRetries: 1 | ||
| } | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,54 @@ | ||
| validate_string_is_12bit_int: | ||
| - name: valid_numbers | ||
| inputs: | ||
| number: | ||
| - "5" | ||
| - "0x900" | ||
| - "01" | ||
| - "4095" | ||
| - "0" | ||
| - "072" | ||
| assertions: | ||
| stderr: | ||
| - Input number \(.*\) is valid | ||
| - name: invalid_numbers | ||
| inputs: | ||
| number: | ||
| - "0x1000" | ||
| - "" | ||
| - string | ||
| - this is not a number | ||
| - "000000000011" | ||
| - "-1" | ||
| - "08" | ||
| assertions: | ||
| exit_code: 42 | ||
| stderr: | ||
| - Input number \(.*\) is invalid | ||
| - name: too_big_decimal_fails | ||
| inputs: | ||
| number: | ||
| - "4096" | ||
| - "9999" | ||
| assertions: | ||
| exit_code: 42 | ||
| stderr: | ||
| - Input number \(.*\) interpreted as decimal | ||
| - But number must be less than 4096! | ||
| validate_flag_filter: | ||
| - name: valid_FlagFilter_passes | ||
| inputs: | ||
| flags: | ||
| - include_if_all: "3" | ||
| exclude_if_any: "0xF04" | ||
| include_if_any: "03" | ||
| exclude_if_all: "4095" | ||
| - name: invalid_FlagFilter_fails | ||
| inputs: | ||
| flags: | ||
| - include_if_all: "3" | ||
| exclude_if_any: "0xF04" | ||
| include_if_any: "03" | ||
| exclude_if_all: "" # empty string should trigger a fail | ||
| assertions: | ||
| should_fail: true |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,93 @@ | ||
| read_group_to_string: | ||
| - name: valid_read_groups | ||
| inputs: | ||
| read_group: | ||
| - ID: R1 | ||
| SM: sampleFoo | ||
| - ID: R1 | ||
| SM: sampleFoo | ||
| LB: spaces are allowed in LB | ||
| BC: barcode with a space | ||
| PU: platform_unit | ||
| PL: ILLUMINA | ||
| CN: center_name | ||
| DT: date | ||
| DS: description | ||
| PI: 1 | ||
| PG: program_group | ||
| PM: platform_model | ||
| FO: ACMG | ||
| KS: key_sequence | ||
| assertions: | ||
| outputs: | ||
| validated_read_group: | ||
| - Contains: R1 | ||
| - Contains: sampleFoo | ||
| - name: id_with_spaces | ||
| inputs: | ||
| read_group: | ||
| - ID: ids should not have spaces # this is a problem | ||
| SM: sample_a | ||
| LB: library | ||
| BC: barcode | ||
| PU: platform_unit | ||
| PL: ILLUMINA | ||
| CN: center_name | ||
| DT: date | ||
| DS: description | ||
| PI: 1 | ||
| PG: program_group | ||
| PM: platform_model | ||
| FO: ACMG | ||
| KS: key_sequence | ||
| assertions: | ||
| should_fail: true | ||
| - name: sample_with_spaces | ||
| inputs: | ||
| read_group: | ||
| - ID: R123 | ||
| SM: samples should not have spaces | ||
| LB: library can have spaces though | ||
| BC: barcode | ||
| PU: platform_unit | ||
| PL: ILLUMINA | ||
| CN: center_name | ||
| DT: date | ||
| DS: description | ||
| PI: 1 | ||
| PG: program_group | ||
| PM: platform_model | ||
| FO: ACMG | ||
| KS: key_sequence | ||
| assertions: | ||
| should_fail: true | ||
| - name: spaces_allowed | ||
| inputs: | ||
| read_group: | ||
| - ID: technically permissable but gross | ||
| SM: same here! | ||
| restrictive: | ||
| - false | ||
| - name: missing_sample | ||
| inputs: | ||
| read_group: | ||
| - ID: R123 | ||
| LB: library | ||
| assertions: | ||
| should_fail: true | ||
| - name: missing_sample_allowed | ||
| inputs: | ||
| read_group: | ||
| - ID: R1 | ||
| LB: lib | ||
| required_fields: | ||
| - [] | ||
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| get_read_groups: | ||
| - name: works | ||
| inputs: | ||
| bam: | ||
| - bams/test.bwa_aln_pe.chrY_chrM.bam | ||
| - bams/Aligned.sortedByCoord.chr9_chr22.bam | ||
| - bams/test_rnaseq_variant.bam | ||
| - bams/test.bam |
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I haven't gotten further, but my assumption was that we'd call
sprocket dev testas the second part of this to test the newly built images.