Fix lint CI: snakefmt smk files + .tests-relative samples path

- snakefmt 2.0.0 reflow of align.smk and common.smk (formatting job)
- config_basic samples path made .tests-relative so it resolves under
  the lint action's directory: .tests (was double-prefixed to
  .tests/.tests/... -> FileNotFoundError at Snakefile:19)

Author: riasc

.tests/integration/config_basic/config.yaml

@@ -6,7 +6,7 @@ threads: 30
 mapq: 30  # overall required mapping quality
 basequal: 20  # overall required base quality 
 
-samples: .tests/integration/config_basic/samples.tsv
+samples: integration/config_basic/samples.tsv
 
 ### pre-processing (only applied on fastq reads)
 preproc:

workflow/rules/align.smk

@@ -228,11 +228,11 @@ rule realign:
         bam="results/{sample}/{seqtype}/align/{group}_final_BWA.bam",
     log:
         "logs/{sample}/align/realign_{seqtype}_{group}.log",
+    wildcard_constraints:
+        seqtype="rnaseq",
     conda:
         "../envs/basic.yml"
     threads: config["threads"]
-    wildcard_constraints:
-        seqtype="rnaseq",
     shell:
         """
         (
@@ -294,9 +294,7 @@ rule dnaseq_final_BWA_stage:
 rule bwa_align_dnaseq:
     input:
         reads=get_dna_align_input,
-        idx=multiext(
-            "resources/refs/bwa/genome", ".amb", ".ann", ".bwt", ".pac", ".sa"
-        ),
+        idx=multiext("resources/refs/bwa/genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
     output:
         "results/{sample}/dnaseq/align/{group}_aligned_BWA.bam",
     log:

workflow/rules/common.smk

@@ -613,7 +613,9 @@ print_run_summary(config, SAMPLES)
 ########### PREPROCESSING ##########
 def get_raw_reads(wildcards):
     if SAMPLES[wildcards.sample]["rnaseq_readtype"] == "SE":
-        return dict(zip(["sample"], SAMPLES[wildcards.sample]["rnaseq"][wildcards.group]))
+        return dict(
+            zip(["sample"], SAMPLES[wildcards.sample]["rnaseq"][wildcards.group])
+        )
 
 
 # returns raw reads for a given sample
@@ -953,7 +955,9 @@ def get_rnaseq_star_bam(wildcards):
 
 def get_star_input(wildcards):
     if SAMPLES[wildcards.sample]["rnaseq_filetype"] == ".bam":
-        return dict(zip(["bam"], [SAMPLES[wildcards.sample]["rnaseq"][wildcards.group]]))
+        return dict(
+            zip(["bam"], [SAMPLES[wildcards.sample]["rnaseq"][wildcards.group]])
+        )
 
     elif (
         SAMPLES[wildcards.sample]["rnaseq_filetype"] == ".fq"
@@ -1440,26 +1444,25 @@ def get_prioritization_proteins(wildcards):
 def get_prioritization_mhcI(wildcards):
     alleles = []
     if config["prioritization"]["class"] in ["I", "BOTH"]:
-        alleles += expand(
-            "results/{sample}/hla/mhc-I.tsv", sample=wildcards.sample
-        )
+        alleles += expand("results/{sample}/hla/mhc-I.tsv", sample=wildcards.sample)
 
     return alleles
 
 
 def get_prioritization_mhcII(wildcards):
     alleles = []
     if config["prioritization"]["class"] in ["II", "BOTH"]:
-        alleles += expand(
-            "results/{sample}/hla/mhc-II.tsv", sample=wildcards.sample
-        )
+        alleles += expand("results/{sample}/hla/mhc-II.tsv", sample=wildcards.sample)
     return alleles
 
 
 def get_prioritization_counts(wildcards):
     counts = []
     # counts can only be generated if either RNAseq or DNAseq data is provided
-    if len(SAMPLES[wildcards.sample]["rnaseq"]) != 0 or len(SAMPLES[wildcards.sample]["dnaseq"]) != 0:
+    if (
+        len(SAMPLES[wildcards.sample]["rnaseq"]) != 0
+        or len(SAMPLES[wildcards.sample]["dnaseq"]) != 0
+    ):
 
         # make sure indels are called from rnaseq/dnaseq data