minor updates and bug fixes; added minced jar to its rule (issue #42)

README.md

@@ -9,4 +9,6 @@ and a hybrid approach.
 git clone --recurse-submodules https://git-r3lab.uni.lu/susheel.busi/ont_pilot_gitlab
 ```
 
+[About git submodules](https://git-scm.com/book/en/v2/Git-Tools-Submodules)
+
 TODO: other dependencies
\ No newline at end of file

workflow/rules/annotation.smk

@@ -149,7 +149,8 @@ rule annotation_rgi:
 
 rule annotation_casc:
     input:
-        os.path.join(RESULTS_DIR, "assembly/{rtype}/{tool}/ASSEMBLY.fasta")
+        asm=os.path.join(RESULTS_DIR, "assembly/{rtype}/{tool}/ASSEMBLY.fasta"),
+        bin=os.path.join(MOD_DIR, "casc/bin/casc")
     output:
         os.path.join(RESULTS_DIR, "annotation/casc/{rtype}/{tool}/ASSEMBLY.results.txt")
     log:
@@ -160,21 +161,20 @@ rule annotation_casc:
         tool="|".join(ASSEMBLERS)
     threads:
         config["casc"]["threads"]
-    params:
-        path=os.path.join(MOD_DIR, "casc/bin/casc")
     conda:
         os.path.join(ENV_DIR, "casc.yaml")
     shell:
         "(date && "
         # "export PATH={config[casc][path]} && "
         # "export PERL5LIB={config[casc][perl5lib]} && "
-        "export PATH=$PATH:$(dirname {params.path}) && "
-        "casc -i {input} -o $(dirname {output}) -n {threads} --conservative && "
+        "export PATH=$PATH:$(dirname {input.bin}) && "
+        "casc -i {input.asm} -o $(dirname {output}) -n {threads} --conservative && "
         "date) 2> {log.err} > {log.out}"
 
 rule annotation_minced:
     input:
-        os.path.join(RESULTS_DIR, "assembly/{rtype}/{tool}/ASSEMBLY.fasta")
+        asm=os.path.join(RESULTS_DIR, "assembly/{rtype}/{tool}/ASSEMBLY.fasta"),
+        jar=os.path.join(MOD_DIR, "minced/minced.jar")
     output:
         txt=os.path.join(RESULTS_DIR, "annotation/minced/{rtype}/{tool}/ASSEMBLY.results.txt"),
         gff=os.path.join(RESULTS_DIR, "annotation/minced/{rtype}/{tool}/ASSEMBLY.results.gff")
@@ -188,8 +188,9 @@ rule annotation_minced:
         os.path.join(ENV_DIR, "minced.yaml")
     shell:
         "(date && "
-        "export PATH={config[minced][path]} && "
-        "minced {input} {output.txt} {output.gff} && "
+        # "export PATH={config[minced][path]} && "
+        "export PATH=$PATH:$(dirname {input.jar}) && "
+        "minced {input.asm} {output.txt} {output.gff} && "
         "date) 2> {log.err} > {log.out}"
 
 ##################################################
@@ -235,6 +236,6 @@ rule annotation_plasflow:
         "PlasFlow: predict: {input}"
     shell:
         "(date && "
-        "PlasFlow.py --input {input} --output {output.tmp} --threshold {params.threshold} &> {log} && "
+        "PlasFlow.py --input {input} --output {output.tmp} --threshold {params.threshold} && "
         "cut -f3,4,6- {output.tmp} > {output.tsv} && "
         "date) 2> {log.err} > {log.out}"