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tests: declare class:Collection / collection_type (epigenetics, data-fetching, chem, read-prep) #1290

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Merged
mvdbeek merged 1 commit into from
Jul 15, 2026
Merged

tests: declare class:Collection / collection_type (epigenetics, data-fetching, chem, read-prep) #1290

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1 change: 1 addition & 0 deletions workflows/computational-chemistry/gromacs-dctmd/gromacs-dctmd-tests.yml
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Expand Up @@ -25,6 +25,7 @@
Salt concentration: 0.1
outputs:
XTC files:
class: Collection
element_tests:
split_file_000000.txt:
assert:
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7 changes: 7 additions & 0 deletions ...ta-and-sequences-from-bioproject-ids/metadata-and-sequences-from-bioproject-ids-tests.yml
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Expand Up @@ -10,10 +10,12 @@
Expand sample attributes in metadata: false
outputs:
SRA metadata table:
class: Collection
element_tests:
PRJNA1417618:
path: test-data/test1_metadata_file_split_file_000000.txt.tsv
Paired End Reads:
class: Collection
element_tests:
SRR37073390:
forward:
Expand All @@ -37,6 +39,7 @@
Expand sample attributes in metadata: false
outputs:
SRA metadata table:
class: Collection
element_tests:
PRJNA1425250:
path: test-data/test2_metadata_file_split_file_000000.txt.tsv
Expand All @@ -45,6 +48,7 @@
path: test-data/test2_metadata_file_split_file_000001.txt.tsv
compare: contains
Paired End Reads:
class: Collection
element_tests:
SRR37273408:
forward:
Expand All @@ -65,6 +69,7 @@
decompress: true
compare: contains
Single End Reads:
class: Collection
element_tests:
SRR37273407:
path: test-data/test2_SRR37273407_forward.fastq
Expand All @@ -83,10 +88,12 @@
Expand sample attributes in metadata: true
outputs:
SRA metadata table:
class: Collection
element_tests:
PRJNA1417618:
path: test-data/test3_metadata.tsv
Paired End Reads:
class: Collection
element_tests:
SRR37073390:
forward:
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3 changes: 3 additions & 0 deletions workflows/data-fetching/parallel-accession-download/parallel-accession-download-tests.yml
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Expand Up @@ -8,6 +8,7 @@
hash_value: 82f7d1a023352b8d99bdf262ccbc0c87723b754b
outputs:
Single End Reads:
class: Collection
element_tests:
SRR044777:
file: test-data/SRR044777_head.fastq
Expand All @@ -24,8 +25,10 @@
hash_value: cc855f075b8473f89364415d7f30fada8182a40a
outputs:
Paired End Reads:
class: Collection
element_tests:
SRR11953971:
class: Collection
elements:
forward:
file: test-data/SRR11953971_1_head.fastq
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4 changes: 4 additions & 0 deletions ...etching/sra-manifest-to-concatenated-fastqs/sra-manifest-to-concatenated-fastqs-tests.yml
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Expand Up @@ -10,8 +10,10 @@
Column number with final identifier: 22
outputs:
paired_output:
class: Collection
element_tests:
GSM461177-:
class: Collection
element_tests:
forward:
asserts:
Expand All @@ -24,6 +26,7 @@
value: 307000000
delta: 30000000
GSM461178___a:
class: Collection
element_tests:
forward:
asserts:
Expand All @@ -36,6 +39,7 @@
value: 205000000
delta: 20000000
single_output:
class: Collection
element_tests:
GSM461176.-:
asserts:
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13 changes: 12 additions & 1 deletion workflows/epigenetics/atacseq/atacseq-tests.yml
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Expand Up @@ -5,7 +5,7 @@
collection_type: list:paired
elements:
- class: Collection
type: paired
collection_type: paired
identifier: SRR891268_chr22_enriched
elements:
- identifier: forward
Expand All @@ -28,6 +28,7 @@
Bin size: 1000
outputs:
mapping stats:
class: Collection
element_tests:
SRR891268_chr22_enriched:
asserts:
Expand All @@ -38,32 +39,37 @@
- that: "has_text"
text: "119723 (42.32%) aligned concordantly >1 times"
MarkDuplicates metrics:
class: Collection
element_tests:
SRR891268_chr22_enriched:
asserts:
has_text:
text: "0.02"
BAM filtered rmDup:
class: Collection
element_tests:
SRR891268_chr22_enriched:
asserts:
has_size:
value: 15810403
delta: 1000000
histogram of fragment length:
class: Collection
element_tests:
SRR891268_chr22_enriched:
asserts:
has_size:
value: 47718
delta: 4000
MACS2 narrowPeak:
class: Collection
element_tests:
SRR891268_chr22_enriched:
asserts:
has_n_lines:
n: 237
MACS2 report:
class: Collection
element_tests:
SRR891268_chr22_enriched:
asserts:
Expand All @@ -72,32 +78,37 @@
- that: "has_text"
text: "# total tags in treatment: 261890"
Coverage from MACS2 (bigwig):
class: Collection
element_tests:
SRR891268_chr22_enriched:
asserts:
has_size:
value: 2892925
delta: 200000
1kb around summits:
class: Collection
element_tests:
SRR891268_chr22_enriched:
asserts:
has_n_lines:
n: 220
Nb of reads in summits +-500bp:
class: Collection
element_tests:
SRR891268_chr22_enriched:
asserts:
has_line:
line: "9522"
bigwig_norm:
class: Collection
element_tests:
SRR891268_chr22_enriched:
asserts:
has_size:
value: 1253177
delta: 100000
bigwig_norm2:
class: Collection
element_tests:
SRR891268_chr22_enriched:
asserts:
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1 change: 1 addition & 0 deletions ...epigenetics/average-bigwig-between-replicates/average-bigwig-between-replicates-tests.yml
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Expand Up @@ -35,6 +35,7 @@
bin_size: 50
outputs:
average_bigwigs:
class: Collection
attributes:
collection_type: list
element_tests:
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9 changes: 8 additions & 1 deletion workflows/epigenetics/chipseq-pe/chipseq-pe-tests.yml
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Expand Up @@ -5,7 +5,7 @@
collection_type: list:paired
elements:
- class: Collection
type: paired
collection_type: paired
identifier: wt_H3K4me3
elements:
- identifier: forward
Expand Down Expand Up @@ -42,19 +42,22 @@
has_text_matching:
expression: "wt_H3K4me3\t20[12].0\t0.0\t13\t98.[0-9]*\t93.[0-9]*\t4.5[0-9]*\t0.095[0-9]*\t57.[0-9]*\t95.[0-9]*\t95.[0-9]*\t0.19[0-9]*\t51.0\t51.0"
filtered BAM:
class: Collection
element_tests:
wt_H3K4me3:
asserts:
has_size:
value: 5311841
delta: 500000
MACS2 summits:
class: Collection
element_tests:
wt_H3K4me3:
asserts:
has_n_lines:
n: 13
MACS2 peaks:
class: Collection
element_tests:
wt_H3K4me3:
asserts:
Expand All @@ -65,12 +68,14 @@
- that: "has_text"
text: "# fragments after filtering in treatment: 42745"
MACS2 narrowPeak:
class: Collection
element_tests:
wt_H3K4me3:
asserts:
has_n_lines:
n: 13
MACS2 report:
class: Collection
element_tests:
wt_H3K4me3:
asserts:
Expand All @@ -81,13 +86,15 @@
- that: "has_text"
text: "# fragments after filtering in treatment: 42745"
coverage from MACS2:
class: Collection
element_tests:
wt_H3K4me3:
asserts:
has_size:
value: 568174
delta: 50000
mapping stats:
class: Collection
element_tests:
wt_H3K4me3:
asserts:
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7 changes: 7 additions & 0 deletions workflows/epigenetics/chipseq-sr/chipseq-sr-tests.yml
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Expand Up @@ -32,19 +32,22 @@
has_text_matching:
expression: "wt_H3K4me3\t200.0\t0.0\t9\t98.[0-9]*\t93.[0-9]*\t2.3[0-9]*\t0.049[0-9]*\t57.[0-9]*\t99.[0-9]*\t99.[0-9]*\t0.12[0-9]*\t51.0"
filtered BAM:
class: Collection
element_tests:
wt_H3K4me3:
asserts:
has_size:
value: 2587182
delta: 200000
MACS2 summits:
class: Collection
element_tests:
wt_H3K4me3:
asserts:
has_n_lines:
n: 9
MACS2 peaks:
class: Collection
element_tests:
wt_H3K4me3:
asserts:
Expand All @@ -55,12 +58,14 @@
- that: "has_text"
text: "# tags after filtering in treatment: 44528"
MACS2 narrowPeak:
class: Collection
element_tests:
wt_H3K4me3:
asserts:
has_n_lines:
n: 9
MACS2 report:
class: Collection
element_tests:
wt_H3K4me3:
asserts:
Expand All @@ -71,13 +76,15 @@
- that: "has_text"
text: "# tags after filtering in treatment: 44528"
coverage from MACS2:
class: Collection
element_tests:
wt_H3K4me3:
asserts:
has_size:
value: 563563
delta: 10000
mapping stats:
class: Collection
element_tests:
wt_H3K4me3:
asserts:
Expand Down
1 change: 1 addition & 0 deletions workflows/epigenetics/consensus-peaks/consensus-peaks-atac-cutandrun-tests.yml
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Expand Up @@ -30,6 +30,7 @@
bin_size: 50
outputs:
individual_macs2_narrowPeaks:
class: Collection
element_tests:
rep1:
asserts:
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1 change: 1 addition & 0 deletions workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe-tests.yml
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Expand Up @@ -30,6 +30,7 @@
bin_size: 50
outputs:
individual_macs2_narrowPeaks:
class: Collection
element_tests:
rep1:
asserts:
Expand Down
1 change: 1 addition & 0 deletions workflows/epigenetics/consensus-peaks/consensus-peaks-chip-sr-tests.yml
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Expand Up @@ -30,6 +30,7 @@
bin_size: 50
outputs:
individual_macs2_narrowPeaks:
class: Collection
element_tests:
rep1:
asserts:
Expand Down
3 changes: 2 additions & 1 deletion ...ad-preprocessing/short-read-qc-trimming/short-read-quality-control-and-trimming-tests.yml
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Expand Up @@ -5,7 +5,7 @@
collection_type: list:paired
elements:
- class: Collection
type: paired
collection_type: paired
identifier: pair
elements:
- class: File
Expand All @@ -29,6 +29,7 @@
- that: has_text
text: "pair"
fastp JSON report:
class: Collection
element_tests:
pair:
asserts:
Expand Down
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