fix: pydeseq2 (#52)

* fix: fixed read filter.py for read_length=0

* feat: samples lookup through params

* fix: renamed tsv to all_counts

* chore: removed 3 bad samples

* debug: until heatmap

* fix: could not get the workflow to work without this insane amount of memory

* feat: demanding correlation matrix and normalized counts (as csv) as outputs

* fix: requireing bam as input

* feat: working again, saver, needs cleaning up

* fix: removed unnecessary R scripts

* style: formatting + removed print statements

* style: snakefmt

---------

Co-authored-by: Yannic Eising <yeising@students.uni-mainz.de>

config/Mainz-MogonNHR/samples.csv

@@ -8,6 +8,6 @@ m18_bc06    male    condition2	batch1          NANOPORE    1
 ma_bc07     male    condition2	batch2          NANOPORE    1
 ma_bc08     male    condition2	batch2          NANOPORE    1
 ma_bc09     female  condition2	batch2          NANOPORE    1
-ma_bc10     male    condition2	batch2          NANOPORE    1
-ma_bc11     male    condition2	batch2          NANOPORE    1
-ma_bc12     female  condition2	batch2          NANOPORE    1
+#ma_bc10     male    condition2	batch2          NANOPORE    1
+#ma_bc11     male    condition2	batch2          NANOPORE    1
+#ma_bc12     female  condition2	batch2          NANOPORE    1

workflow/Snakefile

@@ -198,14 +198,17 @@ rule write_de_params:
 rule de_analysis:
     input:
         de_params=rules.write_de_params.output.de_params,
-        coldata=rules.write_coldata.output.coldata,
-        tsv=rules.merge_counts.output,
+        all_counts=rules.merge_counts.output,
     output:
         dispersion_graph="de_analysis/dispersion_graph.svg",
         ma_graph="de_analysis/ma_graph.svg",
         de_heatmap="de_analysis/heatmap.svg",
+        correlation_matrix="de_analysis/correlation_matrix.svg",
+        normalized_counts="de_analysis/normalized_counts.csv",
         de_top_heatmap="de_analysis/heatmap_top.svg",
         lfc_analysis="de_analysis/lfc_analysis.csv",
+    params:
+        samples=samples,
     log:
         "logs/de_analysis.log",
     threads: 4

workflow/profile/Mainz-MogonNHR/config.yaml

@@ -41,7 +41,7 @@ set-resources:
 
     sam_sort:
         cpus_per_task: 4
-        mem_mb_per_cpu: 3600
+        mem_mb_per_cpu: 7200
         runtime: "2h"
 
     sam_view:

workflow/rules/qc.smk

@@ -128,7 +128,7 @@ rule sam_sort:
 
 rule map_qc:
     input:
-        sorted_bam=rules.sam_sort.output,
+        bam=rules.sam_sort.output,
     output:
         directory("QC/qualimap/{sample}"),
     log: