updated ganges config files; fixed a bug in init.smk and basecalling.smk

config/ganges/config.yaml

@@ -2,7 +2,7 @@
 # STEPS
 
 # Pipeline steps to be done: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
-steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
+steps: ["preprocessing"]
 
 ############################################################
 # INPUT

config/ganges/sbatch.sh

@@ -4,7 +4,7 @@
 # SLURM
 # NOTE: used for this script only, NOT for the snakemake call below
 
-#SBATCH -J ONT_pilot
+#SBATCH -J ONT_SMK
 #SBATCH -N 1
 #SBATCH -n 1
 #SBATCH -c 1
@@ -16,7 +16,7 @@
 # SNAKEMAKE
 
 # conda env name
-ONTP_ENV="snakemake" # USER INPUT REQUIRED
+ONTP_ENV="ONT_pilot"
 # number of cores for snakemake
 ONTP_CORES=60
 # snakemake file
@@ -24,7 +24,7 @@ ONTP_SMK="workflow/Snakefile"
 # config file
 ONTP_CONFIG="config/ganges/config.yaml" # USER INPUT REQUIRED
 # slurm config file
-ONTP_SLURM="config/slurm.yaml"
+ONTP_SLURM="config/ganges/slurm.yaml"
 # slurm cluster call
 ONTP_CLUSTER="-p {cluster.partition} -q {cluster.qos} {cluster.explicit} -N {cluster.nodes} -n {cluster.n} -c {threads} -t {cluster.time} --job-name={cluster.job-name}"
 
@@ -35,6 +35,6 @@ ONTP_CLUSTER="-p {cluster.partition} -q {cluster.qos} {cluster.explicit} -N {clu
 conda activate ${ONTP_ENV}
 
 # run the pipeline
-snakemake --rerun-incomplete -s ${ONTP_SMK} -rp --cores ${ONTP_CORES} --configfile ${ONTP_CONFIG} \
+snakemake -s ${ONTP_SMK} -rp --cores ${ONTP_CORES} --configfile ${ONTP_CONFIG} \
 --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline \
 --cluster-config ${ONTP_SLURM} --cluster "sbatch ${ONTP_CLUSTER}"

config/ganges/slurm.yaml

@@ -5,7 +5,7 @@ __default__:
     nodes: 1
     n: 1
     explicit: ""
-    job-name: "ONT_pilot.{rule}"
+    job-name: "ONT_GANGES.{rule}"
     # output: "slurm-%j.%N-%x.out"
     # error: "slurm-%j.%N-%x.err"
     # mail-type: "end"

workflow/rules/basecalling.smk

@@ -15,7 +15,7 @@ checkpoint guppy_gpu_basecalling:
     shell:
         """
         (date && \
-        {config[guppy][gpu][bin]} --input_path $(dirname {input[0]}) --save_path {output} \
+        {config[guppy][gpu][bin]} --input_path {input} --save_path {output} \
         --config {config[guppy][config]} \
         --disable_pings --compress_fastq \
         --cpu_threads_per_caller {threads} \

workflow/rules/init.smk

@@ -65,6 +65,8 @@ rule link_input_files:
         from pathlib import Path
         # metaG, FAST5
         if not NO_BASECALLING:
+            if not os.path.exists(os.path.join(RESULTS_DIR, "input/metag/ont")):
+                os.makedirs(os.path.join(RESULTS_DIR, "input/metag/ont"))
             for ifname in config["data"]["metag"]["ont"]["files"]:
                 ofname = os.path.join(RESULTS_DIR, "input/metag/ont", os.path.basename(ifname))
                 os.symlink(os.path.abspath(ifname), ofname, target_is_directory=False)
@@ -79,9 +81,9 @@ rule link_input_files:
             os.symlink(os.path.abspath(ifname), ofname, target_is_directory=False)
         # metaG, SR
         os.symlink(os.path.abspath(config["data"]["metag"]["sr"]["r1"]), os.path.join(RESULTS_DIR, "input/metag/sr/R1.fq.gz"), target_is_directory=False)
-        os.symlink(os.path.abspath(config["data"]["metag"]["sr"]["r2"]), os.path.join(RESULTS_DIR, "input/metag/sr/R1.fq.gz"), target_is_directory=False)
+        os.symlink(os.path.abspath(config["data"]["metag"]["sr"]["r2"]), os.path.join(RESULTS_DIR, "input/metag/sr/R2.fq.gz"), target_is_directory=False)
         # metaT, SR
         if "metat" in META_TYPES:
             os.symlink(os.path.abspath(config["data"]["metat"]["sr"]["r1"]), os.path.join(RESULTS_DIR, "input/metat/sr/R1.fq.gz"), target_is_directory=False)
-            os.symlink(os.path.abspath(config["data"]["metat"]["sr"]["r2"]), os.path.join(RESULTS_DIR, "input/metat/sr/R1.fq.gz"), target_is_directory=False)
+            os.symlink(os.path.abspath(config["data"]["metat"]["sr"]["r2"]), os.path.join(RESULTS_DIR, "input/metat/sr/R2.fq.gz"), target_is_directory=False)
     
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