add haploflow

resources/auxiliary_workflows/benchmark/resources/method_definitions/haploflow.py

@@ -0,0 +1,69 @@
+# GROUP: global
+
+"""
+Installation from source, no conda enviroment
+module load stack/2024-06 gcc/12.2.0 openmpi/4.1.6 boost/1.83.0 cmake/3.27.7
+. /cluster/work/bewi/members/lfuhrmann/miniconda3/bin/activate
+cd /cluster/work/bewi/members/lfuhrmann/
+conda activate snakemake
+module load eth_proxy
+"""
+
+import subprocess
+from pathlib import Path
+import os
+
+def main(
+    fname_bam,
+    fname_reference,
+    fname_results_snv,
+    fname_result_haplos,
+    dname_work,
+    seq_type,
+    threads,
+):
+    dname_work.mkdir(parents=True, exist_ok=True)
+
+    fname_fastq = str(fname_bam.resolve()).split(".bam")[0] + ".fastq"
+
+    contig_len_filter = 240  # default of Haploflow: 500
+    error_rate = 0.0199999996 # default for Illumina
+    if seq_type != "illumina":
+        error_rate = 0.1 # for long reads
+
+    # execute tool
+    subprocess.run(
+        [
+            "/cluster/work/bewi/members/lfuhrmann/Haploflow/build/haploflow",
+            "--read-file",
+            fname_fastq,
+            "--out",
+            dname_work,
+            "--log",
+            str((dname_work / "log").resolve()),
+            "--filter",
+            str(contig_len_filter),
+            "--error-rate",
+            str(error_rate),
+            ]
+                )
+
+    fname_haplodmf = dname_work / "contigs.fa"
+    os.rename(fname_haplodmf.resolve(), fname_result_haplos.resolve())
+
+    # create empty vcf files
+    f = open(fname_results_snv, "a")
+    f.write("#CHROM POS ID  REF ALT QUAL    FILTER  INFO")
+    f.close()
+
+
+if __name__ == "__main__":
+    main(
+        Path(snakemake.input.fname_bam),
+        Path(snakemake.input.fname_reference),
+        Path(snakemake.output.fname_result),
+        Path(snakemake.output.fname_result_haplos),
+        Path(snakemake.output.dname_work),
+        snakemake.wildcards.seq_tech,
+        snakemake.threads,
+    )