# Galaxy workflow tests for galaxy-workflow.gxwf.yml # # Two cases: # 1. scf1-both-contrasts-200k -- the biological case. Six ENA runs at 200,000 read pairs. # 2. topology-smoke-25k -- structural smoke test at 25,000 read pairs, no biology. # # READ FIXTURES. test-data/*.fastq.gz (200k) and test-data/smoke-25k/*.fastq.gz (25k) are # deterministic head subsets of the six PRJNA904261 runs, produced by # curl -L | gzip -dc | head -n 800000 (200k pairs; -n 100000 for 25k pairs) # and gzipped with `gzip -n`. Each 200k .fastq was verified byte-for-byte against the # UNCOMPRESSED md5 pinned in test-data-refs.json before compression -- all twelve matched -- # and that md5 is the regeneration check, because gzip output is not byte-stable across gzip # versions. The 25k set was then derived locally as the first 100,000 lines of each VERIFIED # 200k .fastq, which is identical to re-streaming the ENA source with `head -n 100000`. The # SHA-1 values in the `hashes:` blocks below are of the .gz artifacts as produced here and # are the fetch-integrity check. Both are needed and they check different things. If these # fixtures are published (Zenodo), replace each `path:` with the published `location:` and # keep the SHA-1 unchanged -- it pins exactly these bytes. # # REFERENCE. Genome FASTA and GTF are pinned NCBI FTP URLs staged with `decompress: true`. # They carry NO `hashes:` block: test-data-refs.json pins md5s of the COMPRESSED files as # served, and whether a `hashes:` block on a `decompress: true` input checks the fetched or # the decompressed bytes was not established. Omitting is the resolution the test plan # names for that case (unresolved `hash-vs-decompress-ordering`). # # SETTLED HERE, FROM THE PINNED WRAPPER SOURCES (both are the versions this workflow pins). # * featurecounts 2.1.1+galaxy1 builds output_short as `grep -v "^#" output | cut -f 1,7`, # which strips only the "# Program:" comment and keeps the header row, renamed to the # element identifier. output_short is therefore 1 header + one row per annotated gene. # The NCBI GTF for GCA_002759435.2 carries exactly 5586 distinct gene_id values, all of # them matching B9J08_[0-9]{6} -- hence has_n_lines n: 5587 and the annotation guard. # * deseq2 2.11.40.8+galaxy4's deseq2.R writes counts_out with `col.names = NA`, so its # header is padded with a leading blank field: 4 samples -> 5 tab-separated fields on # line 1. has_n_columns n: 5 on both normalized-counts tables is therefore verified, # not assumed, and the test plan's `normalized-counts-header-width-unverified` is closed. # * Both wrappers name count columns by $file.element_identifier, so the normalized-counts # header really does carry AR0382_A / AR0382_tnSWI1_A and the sample-name assertions # below are well founded (test plan's `normalized-counts-column-naming-assumed`, closed). # # HEADER ASYMMETRY. deseq2.R writes `deseq_out` with col.names = FALSE (NO header, which is # why the significance filters bind header_lines: '0') and `counts_out` with col.names = NA # (header present, padded with a leading blank field). The assertions below respect that: # `not_has_text: baseMean` on the raw result tables, sample-name `has_text` on the # normalized-counts tables. # # NOT ASSERTED, DELIBERATELY. No rank claim (SCF1 is 5th/4th by padj and 2nd/1st by # |log2FC| in the two contrasts -- no rank-1 assertion is true in both, and tests-format # cannot express a rank anyway). No exact DESeq2 value, no exact per-gene count, not the # paper's ~29-fold magnitude, and not the negative ALS / IFF-HYR adhesin claim. See the # test plan's omissions[] for each refusal. - doc: >- End-to-end run over all six deposited runs of PRJNA904261 (SRP409192), each subset to the first 200,000 read pairs, against the NCBI GCA_002759435.2 (Cand_auris_B8441_V2) reference and its own GTF. Exercises the whole DAG - flatten side-branch, FastQC, Cutadapt, RNA STAR with a history reference, featureCounts, the sample-sheet condition split, both DESeq2 reductions and both two-link significance chains - and asserts the paper's central result: SCF1 (B9J08_001458) is significantly down-regulated in BOTH contrasts against the AR0382 reference level. Membership in each significant-genes table means padj < 0.05 AND |log2FC| > 1 by construction; the extra floor asserted here is log2FC <= -2. No rank and no measured value is asserted anywhere: the grounding measurements come from pydeseq2 over bwa-mem counts, not from this workflow's R DESeq2 over featureCounts -s 2, so only margins survive the difference. job: RNA-seq reads (sample sheet): class: Collection collection_type: sample_sheet:paired # rows is a mapping of element identifier -> POSITIONAL LIST of column values, # ordered to match the input's column_definitions (condition, replicate). # Not a dict of column-name -> value: validate_row() zips row against # column_definitions and rejects on length mismatch. rows: AR0382_A: [AR0382, A] AR0382_B: [AR0382, B] AR0387_A: [AR0387, A] AR0387_B: [AR0387, B] AR0382_tnSWI1_A: [tnSWI1, A] AR0382_tnSWI1_B: [tnSWI1, B] elements: - class: Collection collection_type: paired identifier: AR0382_A elements: - class: File identifier: forward path: test-data/AR0382_A_1.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: 81847033e7a1bd1430efc68499b08ec2a3de619e - class: File identifier: reverse path: test-data/AR0382_A_2.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: bc59eb5c253f42454631792d59405a019c56dcfe - class: Collection collection_type: paired identifier: AR0382_B elements: - class: File identifier: forward path: test-data/AR0382_B_1.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: a11438bf4c886b081b887ca650642bf925014177 - class: File identifier: reverse path: test-data/AR0382_B_2.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: ab93048b0e16a0729fb0e38ed206cf398ed798df - class: Collection collection_type: paired identifier: AR0387_A elements: - class: File identifier: forward path: test-data/AR0387_A_1.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: 0bcb624b2347148ab740c81ebcb19894449c30b4 - class: File identifier: reverse path: test-data/AR0387_A_2.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: 4590862aba8082c42557f31cbe62c12d694de4b6 - class: Collection collection_type: paired identifier: AR0387_B elements: - class: File identifier: forward path: test-data/AR0387_B_1.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: f0e1a1e97ab993d91baf38ae4ffdd3edf5028905 - class: File identifier: reverse path: test-data/AR0387_B_2.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: 7ccf13c15a7a0ac4571bd2b06796243050d4a17c - class: Collection collection_type: paired identifier: AR0382_tnSWI1_A elements: - class: File identifier: forward path: test-data/AR0382_tnSWI1_A_1.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: 8c76f5caecf41f7a9e62689f5cbdac2e877c31c7 - class: File identifier: reverse path: test-data/AR0382_tnSWI1_A_2.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: 8d8d57b28c41d50a6f5dd13074440deeb801d1da - class: Collection collection_type: paired identifier: AR0382_tnSWI1_B elements: - class: File identifier: forward path: test-data/AR0382_tnSWI1_B_1.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: d666ddad269a39d17b736079f15d5fb98d980851 - class: File identifier: reverse path: test-data/AR0382_tnSWI1_B_2.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: 7a7d6932aed4f46604cd030b04eab9355106e5f9 Reference genome FASTA: class: File location: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/759/435/GCA_002759435.2_Cand_auris_B8441_V2/GCA_002759435.2_Cand_auris_B8441_V2_genomic.fna.gz filetype: fasta decompress: true Gene annotation GTF: class: File location: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/759/435/GCA_002759435.2_Cand_auris_B8441_V2/GCA_002759435.2_Cand_auris_B8441_V2_genomic.gtf.gz filetype: gtf decompress: true Reference condition level: AR0382 First contrast condition level: tnSWI1 Second contrast condition level: AR0387 Strandedness: 'stranded - reverse' Adjusted p-value threshold: 0.05 log2 fold change threshold: 1.0 outputs: 'FastQC raw reads: text summary': class: Collection element_count: 12 element_tests: AR0382_A_forward: asserts: - that: has_text_matching expression: 'Total Sequences\s+200000\b' - that: has_text text: '>>Basic Statistics' AR0382_A_reverse: asserts: - that: has_text_matching expression: 'Total Sequences\s+200000\b' - that: has_text text: '>>Basic Statistics' AR0382_B_forward: asserts: - that: has_text_matching expression: 'Total Sequences\s+200000\b' - that: has_text text: '>>Basic Statistics' AR0382_B_reverse: asserts: - that: has_text_matching expression: 'Total Sequences\s+200000\b' - that: has_text text: '>>Basic Statistics' AR0387_A_forward: asserts: - that: has_text_matching expression: 'Total Sequences\s+200000\b' - that: has_text text: '>>Basic Statistics' AR0387_A_reverse: asserts: - that: has_text_matching expression: 'Total Sequences\s+200000\b' - that: has_text text: '>>Basic Statistics' AR0387_B_forward: asserts: - that: has_text_matching expression: 'Total Sequences\s+200000\b' - that: has_text text: '>>Basic Statistics' AR0387_B_reverse: asserts: - that: has_text_matching expression: 'Total Sequences\s+200000\b' - that: has_text text: '>>Basic Statistics' AR0382_tnSWI1_A_forward: asserts: - that: has_text_matching expression: 'Total Sequences\s+200000\b' - that: has_text text: '>>Basic Statistics' AR0382_tnSWI1_A_reverse: asserts: - that: has_text_matching expression: 'Total Sequences\s+200000\b' - that: has_text text: '>>Basic Statistics' AR0382_tnSWI1_B_forward: asserts: - that: has_text_matching expression: 'Total Sequences\s+200000\b' - that: has_text text: '>>Basic Statistics' AR0382_tnSWI1_B_reverse: asserts: - that: has_text_matching expression: 'Total Sequences\s+200000\b' - that: has_text text: '>>Basic Statistics' Cutadapt trimming report: class: Collection element_count: 6 element_tests: AR0382_A: asserts: - that: has_text_matching expression: 'Total read pairs processed:\s+200,000' AR0382_B: asserts: - that: has_text_matching expression: 'Total read pairs processed:\s+200,000' AR0387_A: asserts: - that: has_text_matching expression: 'Total read pairs processed:\s+200,000' AR0387_B: asserts: - that: has_text_matching expression: 'Total read pairs processed:\s+200,000' AR0382_tnSWI1_A: asserts: - that: has_text_matching expression: 'Total read pairs processed:\s+200,000' AR0382_tnSWI1_B: asserts: - that: has_text_matching expression: 'Total read pairs processed:\s+200,000' Trimmed reads: class: Collection element_count: 6 element_tests: AR0382_A: class: Collection elements: forward: asserts: - that: has_size min: 1000 reverse: asserts: - that: has_size min: 1000 AR0382_B: class: Collection elements: forward: asserts: - that: has_size min: 1000 reverse: asserts: - that: has_size min: 1000 AR0387_A: class: Collection elements: forward: asserts: - that: has_size min: 1000 reverse: asserts: - that: has_size min: 1000 AR0387_B: class: Collection elements: forward: asserts: - that: has_size min: 1000 reverse: asserts: - that: has_size min: 1000 AR0382_tnSWI1_A: class: Collection elements: forward: asserts: - that: has_size min: 1000 reverse: asserts: - that: has_size min: 1000 AR0382_tnSWI1_B: class: Collection elements: forward: asserts: - that: has_size min: 1000 reverse: asserts: - that: has_size min: 1000 STAR mapping summary: class: Collection element_count: 6 element_tests: AR0382_A: asserts: - that: has_text text: 'Uniquely mapped reads %' - that: has_line_matching expression: '\s*Uniquely mapped reads % \|\s+(?:8[0-9]|9[0-9]|100)\.[0-9]+%' AR0382_B: asserts: - that: has_text text: 'Uniquely mapped reads %' - that: has_line_matching expression: '\s*Uniquely mapped reads % \|\s+(?:8[0-9]|9[0-9]|100)\.[0-9]+%' AR0387_A: asserts: - that: has_text text: 'Uniquely mapped reads %' - that: has_line_matching expression: '\s*Uniquely mapped reads % \|\s+(?:8[0-9]|9[0-9]|100)\.[0-9]+%' AR0387_B: asserts: - that: has_text text: 'Uniquely mapped reads %' - that: has_line_matching expression: '\s*Uniquely mapped reads % \|\s+(?:8[0-9]|9[0-9]|100)\.[0-9]+%' AR0382_tnSWI1_A: asserts: - that: has_text text: 'Uniquely mapped reads %' - that: has_line_matching expression: '\s*Uniquely mapped reads % \|\s+(?:8[0-9]|9[0-9]|100)\.[0-9]+%' AR0382_tnSWI1_B: asserts: - that: has_text text: 'Uniquely mapped reads %' - that: has_line_matching expression: '\s*Uniquely mapped reads % \|\s+(?:8[0-9]|9[0-9]|100)\.[0-9]+%' Gene counts per sample: class: Collection element_count: 6 element_tests: AR0382_A: asserts: - that: has_n_columns n: 2 - that: has_n_lines n: 5587 delta: 1 - that: has_line_matching expression: 'B9J08_[0-9]{6}\t[0-9]+' min: 5000 - that: has_line_matching expression: 'B9J08_001458\t[0-9]+' - that: has_line_matching expression: 'B9J08_001458\t[0-9]{3,}' AR0382_B: asserts: - that: has_n_columns n: 2 - that: has_n_lines n: 5587 delta: 1 - that: has_line_matching expression: 'B9J08_[0-9]{6}\t[0-9]+' min: 5000 - that: has_line_matching expression: 'B9J08_001458\t[0-9]+' - that: has_line_matching expression: 'B9J08_001458\t[0-9]{3,}' AR0387_A: asserts: - that: has_n_columns n: 2 - that: has_n_lines n: 5587 delta: 1 - that: has_line_matching expression: 'B9J08_[0-9]{6}\t[0-9]+' min: 5000 - that: has_line_matching expression: 'B9J08_001458\t[0-9]+' - that: has_line_matching expression: 'B9J08_001458\t[0-9]{1,2}' AR0387_B: asserts: - that: has_n_columns n: 2 - that: has_n_lines n: 5587 delta: 1 - that: has_line_matching expression: 'B9J08_[0-9]{6}\t[0-9]+' min: 5000 - that: has_line_matching expression: 'B9J08_001458\t[0-9]+' - that: has_line_matching expression: 'B9J08_001458\t[0-9]{1,2}' AR0382_tnSWI1_A: asserts: - that: has_n_columns n: 2 - that: has_n_lines n: 5587 delta: 1 - that: has_line_matching expression: 'B9J08_[0-9]{6}\t[0-9]+' min: 5000 - that: has_line_matching expression: 'B9J08_001458\t[0-9]+' - that: has_line_matching expression: 'B9J08_001458\t[0-9]{1,2}' AR0382_tnSWI1_B: asserts: - that: has_n_columns n: 2 - that: has_n_lines n: 5587 delta: 1 - that: has_line_matching expression: 'B9J08_[0-9]{6}\t[0-9]+' min: 5000 - that: has_line_matching expression: 'B9J08_001458\t[0-9]+' - that: has_line_matching expression: 'B9J08_001458\t[0-9]{1,2}' featureCounts assignment summary: class: Collection element_count: 6 element_tests: AR0382_A: asserts: - that: has_line_matching expression: 'Assigned\t1[5-9][0-9]{4}' - that: has_line_matching expression: 'Unassigned_NoFeatures\t[0-9]{1,5}' AR0382_B: asserts: - that: has_line_matching expression: 'Assigned\t1[5-9][0-9]{4}' - that: has_line_matching expression: 'Unassigned_NoFeatures\t[0-9]{1,5}' AR0387_A: asserts: - that: has_line_matching expression: 'Assigned\t1[5-9][0-9]{4}' - that: has_line_matching expression: 'Unassigned_NoFeatures\t[0-9]{1,5}' AR0387_B: asserts: - that: has_line_matching expression: 'Assigned\t1[5-9][0-9]{4}' - that: has_line_matching expression: 'Unassigned_NoFeatures\t[0-9]{1,5}' AR0382_tnSWI1_A: asserts: - that: has_line_matching expression: 'Assigned\t1[5-9][0-9]{4}' - that: has_line_matching expression: 'Unassigned_NoFeatures\t[0-9]{1,5}' AR0382_tnSWI1_B: asserts: - that: has_line_matching expression: 'Assigned\t1[5-9][0-9]{4}' - that: has_line_matching expression: 'Unassigned_NoFeatures\t[0-9]{1,5}' 'DESeq2 results: tnSWI1 vs AR0382': asserts: - that: has_n_columns n: 7 - that: not_has_text text: baseMean - that: has_line_matching expression: 'B9J08_001458(\t[^\t]*){6}' - that: has_line_matching expression: 'B9J08_001458\t[^\t]+\t-[0-9.]+(\t[^\t]*){4}' 'DESeq2 results: AR0387 vs AR0382': asserts: - that: has_n_columns n: 7 - that: not_has_text text: baseMean - that: has_line_matching expression: 'B9J08_001458(\t[^\t]*){6}' - that: has_line_matching expression: 'B9J08_001458\t[^\t]+\t-[0-9.]+(\t[^\t]*){4}' 'DESeq2 normalized counts: tnSWI1 vs AR0382': asserts: - that: has_n_columns n: 5 - that: has_line_matching expression: 'B9J08_001458(\t[0-9.eE+-]+){4}' - that: has_text text: AR0382_A - that: has_text text: AR0382_B - that: has_text text: AR0382_tnSWI1_A - that: has_text text: AR0382_tnSWI1_B - that: not_has_text text: AR0387 'DESeq2 normalized counts: AR0387 vs AR0382': asserts: - that: has_n_columns n: 5 - that: has_line_matching expression: 'B9J08_001458(\t[0-9.eE+-]+){4}' - that: has_text text: AR0382_A - that: has_text text: AR0382_B - that: has_text text: AR0387_A - that: has_text text: AR0387_B - that: not_has_text text: tnSWI1 'Significant genes: tnSWI1 vs AR0382': asserts: - that: has_n_columns n: 7 - that: has_line_matching expression: 'B9J08_001458(\t[^\t]*){6}' - that: has_line_matching expression: 'B9J08_001458\t[^\t]+\t-(?:[2-9]|[1-9][0-9]+)(?:\.[0-9]+)?(\t[^\t]*){4}' 'Significant genes: AR0387 vs AR0382': asserts: - that: has_n_columns n: 7 - that: has_line_matching expression: 'B9J08_001458(\t[^\t]*){6}' - that: has_line_matching expression: 'B9J08_001458\t[^\t]+\t-(?:[2-9]|[1-9][0-9]+)(?:\.[0-9]+)?(\t[^\t]*){4}' 'DESeq2 diagnostic plots: tnSWI1 vs AR0382': asserts: - that: has_size min: 10000 'DESeq2 diagnostic plots: AR0387 vs AR0382': asserts: - that: has_size min: 10000 - doc: >- Fast structural smoke test over the same six samples at 25,000 read pairs each (~7 MB compressed total). Makes NO biological claim: at that depth SCF1 falls to roughly 50 fragments in AR0382 and near zero elsewhere, and the significance tables may legitimately be empty. What it does exercise is everything that can silently break without erroring - the sample_sheet:paired input shape, the flatten side-branch, the six-element map-over identifier space, both condition-split joins, both DESeq2 reductions, and both cross-step invariants. Every assertion here is a subset of case 1's, with the depth constant changed and the biological claims removed. job: RNA-seq reads (sample sheet): class: Collection collection_type: sample_sheet:paired # rows is a mapping of element identifier -> POSITIONAL LIST of column values, # ordered to match the input's column_definitions (condition, replicate). # Not a dict of column-name -> value: validate_row() zips row against # column_definitions and rejects on length mismatch. rows: AR0382_A: [AR0382, A] AR0382_B: [AR0382, B] AR0387_A: [AR0387, A] AR0387_B: [AR0387, B] AR0382_tnSWI1_A: [tnSWI1, A] AR0382_tnSWI1_B: [tnSWI1, B] elements: - class: Collection collection_type: paired identifier: AR0382_A elements: - class: File identifier: forward path: test-data/smoke-25k/AR0382_A_1.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: 7686fa073a0089b0376bbe1d3b819b4ea14e3a67 - class: File identifier: reverse path: test-data/smoke-25k/AR0382_A_2.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: f1749c97d907abffd4f5ee36139c22b15376d2af - class: Collection collection_type: paired identifier: AR0382_B elements: - class: File identifier: forward path: test-data/smoke-25k/AR0382_B_1.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: a120941043541873bd674fc8e5cab4bf7d8dcc37 - class: File identifier: reverse path: test-data/smoke-25k/AR0382_B_2.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: 8f315372a23e305fc5dc5ee04d31d8a771ccb8f3 - class: Collection collection_type: paired identifier: AR0387_A elements: - class: File identifier: forward path: test-data/smoke-25k/AR0387_A_1.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: d8e170332a2ae20242b8f79c66f287b79fa2c56a - class: File identifier: reverse path: test-data/smoke-25k/AR0387_A_2.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: 89a32f456f670a00719362b8d72a1a90110c7e94 - class: Collection collection_type: paired identifier: AR0387_B elements: - class: File identifier: forward path: test-data/smoke-25k/AR0387_B_1.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: 022d0851c4b94b919c62d6c1af64e3713bb8e138 - class: File identifier: reverse path: test-data/smoke-25k/AR0387_B_2.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: 28d347eddac1455d3df000846cffb4dc0a472c4d - class: Collection collection_type: paired identifier: AR0382_tnSWI1_A elements: - class: File identifier: forward path: test-data/smoke-25k/AR0382_tnSWI1_A_1.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: 3b6109b5392bba5cb75f312fd7c078b67346013c - class: File identifier: reverse path: test-data/smoke-25k/AR0382_tnSWI1_A_2.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: e5599b61d6ec223f9cd88e7eb7e7877c6d7cf29c - class: Collection collection_type: paired identifier: AR0382_tnSWI1_B elements: - class: File identifier: forward path: test-data/smoke-25k/AR0382_tnSWI1_B_1.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: f803a1ee765bd35a575ab66f80133ad09e50a4ea - class: File identifier: reverse path: test-data/smoke-25k/AR0382_tnSWI1_B_2.fastq.gz filetype: fastqsanger.gz hashes: - hash_function: SHA-1 hash_value: 97a623f6a006e90740a44d6391685ede0157acf4 Reference genome FASTA: class: File location: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/759/435/GCA_002759435.2_Cand_auris_B8441_V2/GCA_002759435.2_Cand_auris_B8441_V2_genomic.fna.gz filetype: fasta decompress: true Gene annotation GTF: class: File location: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/759/435/GCA_002759435.2_Cand_auris_B8441_V2/GCA_002759435.2_Cand_auris_B8441_V2_genomic.gtf.gz filetype: gtf decompress: true Reference condition level: AR0382 First contrast condition level: tnSWI1 Second contrast condition level: AR0387 Strandedness: 'stranded - reverse' Adjusted p-value threshold: 0.05 log2 fold change threshold: 1.0 outputs: 'FastQC raw reads: text summary': class: Collection element_count: 12 element_tests: AR0382_A_forward: asserts: - that: has_text_matching expression: 'Total Sequences\s+25000\b' AR0382_A_reverse: asserts: - that: has_text_matching expression: 'Total Sequences\s+25000\b' AR0382_B_forward: asserts: - that: has_text_matching expression: 'Total Sequences\s+25000\b' AR0382_B_reverse: asserts: - that: has_text_matching expression: 'Total Sequences\s+25000\b' AR0387_A_forward: asserts: - that: has_text_matching expression: 'Total Sequences\s+25000\b' AR0387_A_reverse: asserts: - that: has_text_matching expression: 'Total Sequences\s+25000\b' AR0387_B_forward: asserts: - that: has_text_matching expression: 'Total Sequences\s+25000\b' AR0387_B_reverse: asserts: - that: has_text_matching expression: 'Total Sequences\s+25000\b' AR0382_tnSWI1_A_forward: asserts: - that: has_text_matching expression: 'Total Sequences\s+25000\b' AR0382_tnSWI1_A_reverse: asserts: - that: has_text_matching expression: 'Total Sequences\s+25000\b' AR0382_tnSWI1_B_forward: asserts: - that: has_text_matching expression: 'Total Sequences\s+25000\b' AR0382_tnSWI1_B_reverse: asserts: - that: has_text_matching expression: 'Total Sequences\s+25000\b' Gene counts per sample: class: Collection element_count: 6 element_tests: AR0382_A: asserts: - that: has_n_columns n: 2 - that: has_n_lines n: 5587 delta: 1 - that: has_line_matching expression: 'B9J08_[0-9]{6}\t[0-9]+' min: 5000 AR0382_B: asserts: - that: has_n_columns n: 2 - that: has_n_lines n: 5587 delta: 1 - that: has_line_matching expression: 'B9J08_[0-9]{6}\t[0-9]+' min: 5000 AR0387_A: asserts: - that: has_n_columns n: 2 - that: has_n_lines n: 5587 delta: 1 - that: has_line_matching expression: 'B9J08_[0-9]{6}\t[0-9]+' min: 5000 AR0387_B: asserts: - that: has_n_columns n: 2 - that: has_n_lines n: 5587 delta: 1 - that: has_line_matching expression: 'B9J08_[0-9]{6}\t[0-9]+' min: 5000 AR0382_tnSWI1_A: asserts: - that: has_n_columns n: 2 - that: has_n_lines n: 5587 delta: 1 - that: has_line_matching expression: 'B9J08_[0-9]{6}\t[0-9]+' min: 5000 AR0382_tnSWI1_B: asserts: - that: has_n_columns n: 2 - that: has_n_lines n: 5587 delta: 1 - that: has_line_matching expression: 'B9J08_[0-9]{6}\t[0-9]+' min: 5000 'DESeq2 results: tnSWI1 vs AR0382': asserts: - that: has_n_columns n: 7 - that: not_has_text text: baseMean 'DESeq2 results: AR0387 vs AR0382': asserts: - that: has_n_columns n: 7 - that: not_has_text text: baseMean 'DESeq2 normalized counts: tnSWI1 vs AR0382': asserts: - that: has_n_columns n: 5 - that: has_text text: AR0382_A - that: has_text text: AR0382_B - that: has_text text: AR0382_tnSWI1_A - that: has_text text: AR0382_tnSWI1_B - that: not_has_text text: AR0387 'DESeq2 normalized counts: AR0387 vs AR0382': asserts: - that: has_n_columns n: 5 - that: has_text text: AR0382_A - that: has_text text: AR0382_B - that: has_text text: AR0387_A - that: has_text text: AR0387_B - that: not_has_text text: tnSWI1