path fix; config fix; common env

configs/env/common.yaml

+name: quac_common
+
+channels:
+  - conda-forge
+  - bioconda
+
+dependencies:
+  - python==3.7.6
+  - pandas==1.2.2
+  - numpy==1.19.5
+  - xlrd==1.2.0
+  - ped_parser==1.6.6
+  - fire==0.3.1
+  - colorlog==4.7.2
+  - black==20.8b1

configs/workflow.yaml

 projects_path: "/data/project/worthey_lab/projects/"
-project_names: "MuscDyst_SU_MAlexander,CF_CFF_PFarrell,CF_TLOAF_PFarrell"
+# project_names: "MuscDyst_SU_MAlexander,CF_CFF_PFarrell,CF_TLOAF_PFarrell,EDS3_unkn_DGreenspan,UDN_Phase1_EAWorthey"
+project_names: "CF_CFF_PFarrell"
 ref: "/data/project/worthey_lab/datasets_central/human_reference_genome/processed/GRCh38/no_alt_rel20190408/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna"
 somalier:
     tool: "/data/project/worthey_lab/projects/experimental_pipelines/mana/tools/somalier/0.2.12/somalier"
@@ -10,8 +11,4 @@ goleft:
     tool: "/data/project/worthey_lab/projects/experimental_pipelines/mana/tools/goleft/0.2.4/goleft"
 verifyBamID:
     svd_dat: "/data/project/worthey_lab/projects/experimental_pipelines/mana/test_tools/verifyBamID/tool/VerifyBamID-2.0.1/resource/1000g.phase3.100k.b38.vcf.gz.dat"
-haplocheck:
-    mutserve_tool: "/data/project/worthey_lab/projects/experimental_pipelines/mana/test_tools/haplocheck/mutserve/mutserve"
-    mt_ref: "/data/project/worthey_lab/projects/experimental_pipelines/mana/test_tools/haplocheck/mutserve/rCRS.fasta"
-    haplocheck_tool: "/data/project/worthey_lab/projects/experimental_pipelines/mana/test_tools/haplocheck/tool/haplocheck"
 logs_path: "logs/rule_logs/"

workflow/rules/mosdepth.smk

@@ -3,8 +3,8 @@ 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 = PROCESSED_DIR / "mosdepth/{project}/{sample}.mosdepth.global.dist.txt",
-        summary = PROCESSED_DIR / "mosdepth/{project}/{sample}.mosdepth.summary.txt",
+        dist = INTERIM_DIR / "mosdepth/{project}/{sample}.mosdepth.global.dist.txt",
+        summary = INTERIM_DIR / "mosdepth/{project}/{sample}.mosdepth.summary.txt",
     log:
         LOGS_PATH / "{project}/mosdepth_coverage-{sample}.log"
     message:
@@ -27,7 +27,7 @@ rule mosdepth_coverage:
 
 rule mosdepth_plot:
     input:
-        dist = lambda wildcards: expand(str(PROCESSED_DIR / "mosdepth" / wildcards.project / "{sample}.mosdepth.global.dist.txt"),
+        dist = lambda wildcards: expand(str(INTERIM_DIR / "mosdepth" / wildcards.project / "{sample}.mosdepth.global.dist.txt"),
                 sample=SAMPLES[wildcards.project]),
         script = WORKFLOW_PATH / "src/mosdepth/v0.3.1/plot-dist.py",
     output: