cleans up outpaths

workflow/rules/common.smk

@@ -53,7 +53,7 @@ def get_targets(tool_name, project=PROJECT_NAME, samples=SAMPLES):
     elif tool_name == 'mosdepth':
         flist += expand(str(PROCESSED_DIR / "mosdepth/{project}/mosdepth_{project}.html"),
                     project=[PROJECT_NAME]),
-        flist += expand(str(INTERIM_DIR / "mosdepth/{project}/{sample}.mosdepth.global.dist.txt"),
+        flist += expand(str(PROCESSED_DIR / "mosdepth/{project}/results/{sample}.mosdepth.global.dist.txt"),
                     project=[PROJECT_NAME],
                     sample=SAMPLES),
     elif tool_name == 'verifybamid':

workflow/rules/coverage_analysis.smk

@@ -14,8 +14,8 @@ rule mosdepth_coverage:
         bam = PROJECTS_PATH / "{project}" / "analysis" / "{sample}" / "bam" / "{sample}.bam",
         bam_index = PROJECTS_PATH / "{project}" / "analysis" / "{sample}" / "bam" / "{sample}.bam.bai",
     output:
-        dist = INTERIM_DIR / "mosdepth/{project}/{sample}.mosdepth.global.dist.txt",
-        summary = INTERIM_DIR / "mosdepth/{project}/{sample}.mosdepth.summary.txt",
+        dist = PROCESSED_DIR / "mosdepth/{project}/results/{sample}.mosdepth.global.dist.txt",
+        summary = PROCESSED_DIR / "mosdepth/{project}/results/{sample}.mosdepth.summary.txt",
     message:
         "Running mosdepth for coverage. Project: {wildcards.project}, sample: {wildcards.sample}"
     group:
@@ -39,7 +39,7 @@ rule mosdepth_coverage:
 
 rule mosdepth_plot:
     input:
-        dist = expand(str(INTERIM_DIR / "mosdepth" / "{{project}}" / "{sample}.mosdepth.global.dist.txt"),
+        dist = expand(str(PROCESSED_DIR / "mosdepth" / "{{project}}" / "results" / "{sample}.mosdepth.global.dist.txt"),
                 sample=SAMPLES),
         script = WORKFLOW_PATH / "src/mosdepth/v0.3.1/plot-dist.py",
     output:

workflow/rules/relatedness_ancestry.smk

@@ -10,7 +10,7 @@ rule somalier_extract:
         sites = config['somalier']['sites'],
         ref_genome = config['ref'],
     output:
-        INTERIM_DIR / "somalier_extract/{project}/{sample}.somalier"
+        PROCESSED_DIR / "somalier/{project}/extract/{sample}.somalier",
     message:
         "Running somalier extract. Project: {wildcards.project}"
     group:
@@ -29,14 +29,14 @@ rule somalier_extract:
 
 rule somalier_relate:
     input:
-        extracted = expand(str(INTERIM_DIR / "somalier_extract" / "{{project}}" / "{sample}.somalier"),
+        extracted = expand(str(PROCESSED_DIR / "somalier" / "{{project}}" / "extract" / "{sample}.somalier"),
                 sample=SAMPLES),
         ped = RAW_DIR / "ped" / "{project}.ped",
         somalier_tool = config['somalier']['tool'],
     output:
         out = expand(str(PROCESSED_DIR / "somalier/{{project}}/relatedness/somalier.{ext}"),
                 ext=['html', 'groups.tsv', 'pairs.tsv', 'samples.tsv']),
-        log = PROCESSED_DIR / "somalier/{{project}}/relatedness/somalier.log",
+        log = PROCESSED_DIR / "somalier/{project}/relatedness/somalier.log",
     message:
         "Running somalier relate. Project: {wildcards.project}"
     group:
@@ -59,7 +59,7 @@ rule somalier_relate:
 
 rule somalier_ancestry:
     input:
-        extracted = expand(str(INTERIM_DIR / "somalier_extract" / "{{project}}" / "{sample}.somalier"),
+        extracted = expand(str(PROCESSED_DIR / "somalier" / "{{project}}" / "extract" / "{sample}.somalier"),
                 sample=SAMPLES),
         somalier_tool = config['somalier']['tool'],
         labels_1kg = config['somalier']['labels_1kg'],