Merge pull request #51 from hydra-genetics/develop

chore: dev to master
hydra-genetics · Apr 8, 2022 · f696e17 · f696e17
2 parents bee599e + 530c359
commit f696e17
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Showing 4 changed files with 10 additions and 6 deletions.
diff --git a/.tests/integration/units.tsv b/.tests/integration/units.tsv
@@ -1,4 +1,4 @@
 sample	type	platform	machine	flowcell	lane	barcode	fastq1	fastq2	adapter
-HD827sonic	N	NextSeq	NDX550220	HKTG2BGXG	lane1	ACGGAACA+ACGAGAAC	fastq/HD827sonic_testing1_R1.fastq.gz	fastq/HD827sonic_testing1_R2.fastq.gz	AGATCGGAAGAGCACACGTCTGAACTCCAGTCA,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
-HD827sonic	N	NextSeq	NDX550220	HKTG2BGXG	lane2	ACGGAACA+ACGAGAAC	fastq/HD827sonic_testing2_R1.fastq.gz	fastq/HD827sonic_testing2_R2.fastq.gz	AGATCGGAAGAGCACACGTCTGAACTCCAGTCA,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
-HD827sonic	T	NextSeq	NDX550220	HKTG2BGXG	lane3	ACGGAACA+ACGAGAAC	fastq/HD827sonic_testing3_R1.fastq.gz	fastq/HD827sonic_testing3_R2.fastq.gz	AGATCGGAAGAGCACACGTCTGAACTCCAGTCA,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
+HD827sonic	N	NextSeq	NDX550220	HKTG2BGXG	L001	ACGGAACA+ACGAGAAC	fastq/HD827sonic_testing1_R1.fastq.gz	fastq/HD827sonic_testing1_R2.fastq.gz	AGATCGGAAGAGCACACGTCTGAACTCCAGTCA,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
+HD827sonic	N	NextSeq	NDX550220	HKTG2BGXG	L001	ACGGAACA+ACGAGAAG	fastq/HD827sonic_testing2_R1.fastq.gz	fastq/HD827sonic_testing2_R2.fastq.gz	AGATCGGAAGAGCACACGTCTGAACTCCAGTCA,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
+HD827sonic	T	NextSeq	NDX550220	HKTG2BGXG	L002	ACGGAACA+ACGAGAAT	fastq/HD827sonic_testing3_R1.fastq.gz	fastq/HD827sonic_testing3_R2.fastq.gz	AGATCGGAAGAGCACACGTCTGAACTCCAGTCA,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -45,6 +45,9 @@ validate(units, schema="../schemas/units.schema.yaml")
 
 
 wildcard_constraints:
+    barcode="[A-Z+]+",
+    flowcell="[A-Z0-9]+",
+    lane="L[0-9]+",
     sample="|".join(get_samples(samples)),
     unit="N|T|R",
     read="fastq[1|2]",
@@ -55,8 +58,8 @@ wildcard_constraints:
 
 if config.get("trimmer_software", None) == "fastp_pe":
     merged_input = lambda wildcards: expand(
-        "prealignment/fastp_pe/{{sample}}_{flowcell_lane}_{{type}}_{{read}}.fastq.gz",
-        flowcell_lane=[
+        "prealignment/fastp_pe/{{sample}}_{flowcell_lane_barcode}_{{type}}_{{read}}.fastq.gz",
+        flowcell_lane_barcode=[
             "{}_{}_{}".format(unit.flowcell, unit.lane, unit.barcode) for unit in get_units(units, wildcards, wildcards.type)
         ],
     )

diff --git a/workflow/rules/merged.smk b/workflow/rules/merged.smk
@@ -8,7 +8,7 @@ rule merged:
     input:
         fastq=merged_input,
     output:
-        fastq="prealignment/merged/{sample}_{type}_{read}.fastq.gz",
+        fastq=temp("prealignment/merged/{sample}_{type}_{read}.fastq.gz"),
     log:
         "prealignment/merged/{sample}_{type}_{read}.fastq.gz.log",
     benchmark:

diff --git a/workflow/schemas/units.schema.yaml b/workflow/schemas/units.schema.yaml
@@ -23,6 +23,7 @@ properties:
   lane:
     type: string
     description: lane number
+    pattern: "^L[0-9]+$"
   fastq1:
     type: string
     description: absolute path to R1 fastq file