Debug mitoz_annotate (multiples fastqs)

Debug circos (increase max_points_per_track)

Mito_Assembler_Megahit/Dockerfile

@@ -30,7 +30,8 @@ RUN apt-get install -y circos \
  && cd /opt/biotools && wget http://circos.ca/distribution/circos-current.tgz \
  && tar -xzf circos-current.tgz \
  && rm -rf circos-current.tgz \
- && mv circos* circos_current
+ && mv circos* circos_current \
+ && sed -i 's/max_points_per_track.*/max_points_per_track = 40000/' /opt/biotools/circos_current/etc/housekeeping.conf
 
 RUN cd /opt/biotools \
  && wget https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2 \

Mito_Assembler_Megahit/files/Snakefile

@@ -287,7 +287,7 @@ rule mitoz_annotate_SE:
         clade = config["clade"],
         sample_suffix = config["sample_suffix"]
     shell:
-        "cat {input.read} > reads_R1.{params.sample_suffix} "
+        "cat {input.read} > {params.results_dir}/reads_R1.{params.sample_suffix} "
         "&& /opt/biotools/release_MitoZ_v2.4-alpha/MitoZ.py annotate "
         "--fastq1 reads_R1.{params.sample_suffix} "
         #"--fq_size 0 "
@@ -319,7 +319,7 @@ rule mitoz_annotate_SE:
         "else \n"
         "   mv circos.png circos_mqc.png \n"
         "fi \n"
-        "rm reads_R1.{params.sample_suffix} "
+        "rm {params.results_dir}/reads_R1.{params.sample_suffix} "
 
 rule mitoz_annotate_PE:
     input:
@@ -338,8 +338,8 @@ rule mitoz_annotate_PE:
         clade = config["clade"],
         sample_suffix = config["sample_suffix"]
     shell:
-        "cat {input.read} > reads_R1.{params.sample_suffix} "
-        "&& cat {input.read2} > reads_R2.{params.sample_suffix} "
+        "cat {input.read} > {params.results_dir}/reads_R1.{params.sample_suffix} "
+        "&& cat {input.read2} > {params.results_dir}/reads_R2.{params.sample_suffix} "
         "&& /opt/biotools/release_MitoZ_v2.4-alpha/MitoZ.py annotate "
         "--fastq1 reads_R1.{params.sample_suffix} "
         "--fastq2 reads_R2.{params.sample_suffix} "
@@ -372,8 +372,8 @@ rule mitoz_annotate_PE:
         "else \n"
         "   mv circos.png circos_mqc.png \n"
         "fi \n"
-        "rm reads_R1.{params.sample_suffix} "
-        "&& rm reads_R2.{params.sample_suffix} "
+        "rm {params.results_dir}/reads_R1.{params.sample_suffix} "
+        "&& rm {params.results_dir}/reads_R2.{params.sample_suffix} "
 
 ruleorder:  mitoz_annotate_PE > mitoz_annotate_SE
 

Mito_Assembler_Megahit/files/singularity.def

@@ -110,6 +110,7 @@ singularity run --app appName this_container.sif
 	rm -rf circos-current.tgz
 	mv circos* circos_current
 	echo 'export PATH="/opt/biotools/circos_current/bin:$PATH"' >>$SINGULARITY_ENVIRONMENT
+	sed -i 's/max_points_per_track.*/max_points_per_track = 40000/' /opt/biotools/circos_current/etc/housekeeping.conf
 
 	cd /opt/biotools
 	wget https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2