WIP: Checkpoint snakefile

2019_GDB/rules/ASSEMBLY_ANNOTATION_RULES

@@ -512,7 +512,8 @@ rule assemble_long_reads_w_flye:
     output: os.path.join(RESULTS_DIR, "assembly/flye/lr/merged/{barcode}/assembly.fna")
     threads: config["flye"]["threads"]
     log: os.path.join(RESULTS_DIR, "assembly/flye/lr/merged/{barcode}/assembly.flye")
-    conda: "../envs/flye.yaml"
+#    conda: "../envs/flye.yaml"
+    conda: "../envs/flye_v2_7.yaml"
     shell:
         """
         (date &&\
@@ -779,6 +780,26 @@ rule assemble_short_reads_w_megahit:
         date) 2> >(tee {log}.stderr) > >(tee {log}.stdout)
         """
 
+rule assemble_short_reads_w_metaspades:
+    input:
+        sr_r1=rules.run_fastp_on_short_reads.output.r1,
+        sr_r2=rules.run_fastp_on_short_reads.output.r2
+    output: os.path.join(RESULTS_DIR, "assembly/metaspades/{sr_sample}/final.contigs.fna")
+    threads: config["metaspades"]["threads"]
+    conda: "../envs/spades.yaml"
+    params:
+        tmp_dir=os.path.join(RESULTS_DIR, "assembly/metaspades/{sr_sample}_tmp")
+    log: os.path.join(RESULTS_DIR, "assembly/metaspades/{sr_sample}/metaspades.log")
+    shell:
+        """
+        (date &&\
+        metaspades.py -k 21,33,55,77 -t {threads} -1 {input.sr_r1} -2 {input.sr_r2} -o {params.tmp_dir} &&\
+        mv {params.tmp_dir}/* $(dirname {output}) &&\
+        rmdir {params.tmp_dir} &&\
+        ln -s contigs.fasta {output} &&\
+        date) 2> >(tee {log}.stderr) > >(tee {log}.stdout)
+        """
+
 # N.B. A similar function exists above and code duplication is generally discouraged.
 rule map_short_reads_to_short_read_contigs_w_bwa_mem:
     input: