for test data, disable macs2 model

workflow/rules/common.smk

@@ -246,11 +246,11 @@ def get_multiqc_input(wildcards):
                     "results/picard_dedup/{sample}.picard_dedup.stats.txt",
                     "results/bamtools_filtered/{sample}.sorted.bamtools_filtered.flagstat",
                     "results/bamtools_filtered/{sample}.sorted.bamtools_filtered.idxstats",
-                    "results/bamtools_filtered/{sample}.sorted.bamtools_filtered.stats.txt",
-                    "results/phantompeakqualtools/{sample}.phantompeak.spp.out",
-                    "results/phantompeakqualtools/{sample}.spp_correlation_mqc.tsv",
-                    "results/phantompeakqualtools/{sample}.spp_nsc_mqc.tsv",
-                    "results/phantompeakqualtools/{sample}.spp_rsc_mqc.tsv"
+                    "results/bamtools_filtered/{sample}.sorted.bamtools_filtered.stats.txt"
+                    #"results/phantompeakqualtools/{sample}.phantompeak.spp.out",
+                    #"results/phantompeakqualtools/{sample}.spp_correlation_mqc.tsv",
+                    #"results/phantompeakqualtools/{sample}.spp_nsc_mqc.tsv",
+                    #"results/phantompeakqualtools/{sample}.spp_rsc_mqc.tsv"
                 ],
                 sample = sample
             )
@@ -338,8 +338,8 @@ def all_input(wildcards):
         if is_single_end(sample, unit):
             wanted_input.extend(expand(
                     [
-                        "results/trimmed_se/{sample}-{unit}.fastq.gz"#,
-                        #"results/trimmed_se/{sample}-{unit}.settings"
+                        "results/trimmed_se/{sample}-{unit}.fastq.gz",
+                        "results/trimmed_se/{sample}-{unit}.settings"
                     ],
                     sample = sample,
                     unit = unit
@@ -349,8 +349,8 @@ def all_input(wildcards):
             wanted_input.extend(
                 expand (
                     [
-                        "results/trimmed_pe/{sample}-{unit}.R1.fastq.gz",
-                        "results/trimmed_pe/{sample}-{unit}.R2.fastq.gz",
+                        "results/trimmed_pe/{sample}-{unit}.1.fastq.gz",
+                        "results/trimmed_pe/{sample}-{unit}.2.fastq.gz",
                         "results/trimmed_pe/{sample}-{unit}.settings"
                     ],
                     sample = sample,
@@ -360,14 +360,14 @@ def all_input(wildcards):
 
     # mapping, merging and filtering bam-files
     for sample in samples.index:
-        wanted_input.extend(
-            expand (
-                [
-                    "results/phantompeakqualtools/{sample}.phantompeak.pdf"
-                ],
-                sample = sample
-            )
-        )
+        #wanted_input.extend(
+        #    expand (
+        #        [
+        #            "results/phantompeakqualtools/{sample}.phantompeak.pdf"
+        #        ],
+        #        sample = sample
+        #    )
+        #)
 
         if config["params"]["deeptools-plots"]["activate"]:
             wanted_input.extend(

workflow/rules/peak_analysis.smk

@@ -57,8 +57,8 @@ rule macs2_callpeak_broad:
                  )
     log:
         "logs/macs2/callpeak.{sample}-{control}.broad.log"
-    params:
-        lambda w, input:"--broad-cutoff 0.1 -f {bam_format} {gsize} -B --SPMR --keep-dup all {pvalue} {qvalue}".format(
+    params:                                                         # --nomodel --extsize 147 added for fake data
+        lambda w, input:"--broad-cutoff 0.1 -f {bam_format} {gsize} --nomodel --extsize 147 -B --SPMR --keep-dup all {pvalue} {qvalue}".format(
             gsize="{}".format(open(input.gsizepath).read().strip()),
             pvalue="-p {}".format(config["params"]["callpeak"]["p-value"]) if config["params"]["callpeak"]["p-value"] else "",
             qvalue="-q {}".format(config["params"]["callpeak"]["q-value"]) if config["params"]["callpeak"]["q-value"] else "",
@@ -217,7 +217,7 @@ rule plot_macs_qc:
     conda:
         "../envs/plot_macs_annot.yaml"
     shell:
-        "Rscript ../workflow/scripts/plot_macs_qc.R -i {params.input} -s {params.sample_control_combinations}  "
+        "Rscript workflow/scripts/plot_macs_qc.R -i {params.input} -s {params.sample_control_combinations}  "
         "-o {output.plot} -p {output.summmary} 2> {log}"
 
 rule plot_homer_annotatepeaks:
@@ -237,7 +237,7 @@ rule plot_homer_annotatepeaks:
     conda:
         "../envs/plot_macs_annot.yaml"
     shell:
-        "Rscript ../workflow/scripts/plot_homer_annotatepeaks.R -i {params.input} "
+        "Rscript workflow/scripts/plot_homer_annotatepeaks.R -i {params.input} "
         "-s {params.sample_control_combinations}  -o {output.plot} -p {output.summmary} 2> {log}"
 
 rule plot_sum_annotatepeaks: