diff --git a/.config/masterconfig.yaml b/.config/masterconfig.yaml
index 827b73d952ae28570bf87aebd6585e1645097ffe..6f0f25a8344588c3800cf3778d2d1232a81e8df4 100644
--- a/.config/masterconfig.yaml
+++ b/.config/masterconfig.yaml
@@ -1,5 +1,5 @@
# absolute path to your desired output path
-root: /output/path
+root: .
####################### optional prejob - data preparation #######################
# path to tar data
diff --git a/.gitignore b/.gitignore
index bef92460568ca779f830417295512f9f81ef0fb6..24af5b9310912a013a8c74ce09628f170a31261f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -51,6 +51,8 @@
!Snakefile
!*.smk
!*.svg
+!slurm_logs/
+
# 3) add a pattern to track the file patterns of section2 even if they are in
# subdirectories
diff --git a/README.md b/README.md
index 7edeb144199b7c6d1533deb4ba23353eaa95cf01..823d88966ccdac8a6bedba262e50446a727824a8 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@ This workflow uses [Snakemake](https://snakemake.readthedocs.io/en/stable/) to q
A first script (```prejob.sh```) prepares the data until *fasta.gz* files are obtained. A second script (```job.sh```) runs the genome assembly and stats.
-doc: [Gitlab pages](https://asm4pg.pages.mia.inra.fr/genomasm4pg)
+doc: [Gitlab pages](https://asm4pg.pages.mia.inra.fr/GenomAsm4pg/)
diff --git a/job.sh b/job.sh
index 88686b0521f4c2737513bf62636571af8b1039ff..1a5b57e377187b5a889ea5afb6a9758f7d05fe4b 100644
--- a/job.sh
+++ b/job.sh
@@ -35,12 +35,23 @@ echo 'scontrol show job:'
scontrol show job $SLURM_JOB_ID
echo '########################################'
+## get SNG_BIND abs path using python
+function SNG_BIND_ABS_PATH {
+ SNG_BIND="$(python3 - <<END
+import os
+
+abs_path = os.getcwd()
+print(abs_path)
+
+END
+)"
+}
+SNG_BIND_ABS_PATH
### variables
CLUSTER_CONFIG=".config/snakemake_profile/slurm/cluster_config.yml"
MAX_CORES=10
PROFILE=".config/snakemake_profile/slurm"
-SNG_BIND="/gpfs/scratch/sdenni/wf/GenomAsm4pg"
### Module Loading:
module purge
@@ -48,8 +59,6 @@ module load snakemake/6.5.1
echo 'Starting Snakemake workflow'
-### create a log directory for slurm output files
-mkdir -p slurm_logs
### Snakemake commands
diff --git a/prejob.sh b/prejob.sh
index d65a60ed5d574cd026944c172bac183f7e9a6c25..ec05113d016405655dd09530a01af9a8c4dce9a7 100644
--- a/prejob.sh
+++ b/prejob.sh
@@ -35,12 +35,25 @@ echo 'scontrol show job:'
scontrol show job $SLURM_JOB_ID
echo '########################################'
+
+## get SNG_BIND abs path using python
+function SNG_BIND_ABS_PATH {
+ SNG_BIND="$(python3 - <<END
+import os
+
+abs_path = os.getcwd()
+print(abs_path)
+
+END
+)"
+}
+SNG_BIND_ABS_PATH
+
### variables
CLUSTER_CONFIG=".config/snakemake_profile/slurm/cluster_config.yml"
MAX_CORES=4
PROFILE=".config/snakemake_profile/slurm"
SMK_PATH="workflow/pre-job_snakefiles"
-SNG_BIND="/gpfs/scratch/sdenni/wf/GenomAsm4pg"
### Module Loading:
module purge
diff --git a/slurm_logs/.gitignore b/slurm_logs/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..5d59d6d0f3388a645844c8f5fc57bcd929a53798
--- /dev/null
+++ b/slurm_logs/.gitignore
@@ -0,0 +1,6 @@
+### This file is here to avoid a SLURM error when running a job because of the missing slurm_logs directory
+
+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore
\ No newline at end of file
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 538fbbae76c55fa1c96e555ffa69b818d0b12511..6bc7660156e16a5af983375cfef64dac68835058 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -1,13 +1,21 @@
configfile: ".config/masterconfig.yaml"
-res_path=config["root"] + "/" + config["resdir"]
-
###### Include all scripts & rules necessary to run the workflow ######
### Scripts
# get parameters from masterconfig
include: "scripts/from_config/hifiasm_mode.py"
include: "scripts/from_config/parameters.py"
include: "scripts/from_config/target_list.py"
+include: "scripts/path_helper.py"
+
+### paths
+if config["root"].startswith("."):
+ abs_root_path = get_abs_root_path()
+ res_path = get_res_path()
+else:
+ abs_root_path = config["root"]
+ res_path = abs_root_path + "/" + config["resdir"]
+
### Rules
## PRE ASSEMBLY QC
@@ -16,11 +24,11 @@ include: "rules/01_qc.smk"
include: "rules/02_asm.smk"
# Statistics
include: "rules/03_asm_qc.smk"
-include: "rules/03.5_A_qc_merqury.smk"
+include: "rules/03.5_asm_qc_merqury.smk"
# Purging
include: "rules/04_purge_dups.smk"
include: "rules/05_purged_asm_qc.smk"
-include: "rules/05.5_PA_qc_merqury.smk"
+include: "rules/05.5_purged_asm_qc_merqury.smk"
#Â Link final assembly
include: "rules/06_sym_link_hap.smk"
## AUTOMATIC REPORT
@@ -39,7 +47,6 @@ BID_RUN = run_BFid(bamIDS)
FID_RUN = run_BFid(fastqIDS)
###### results path ######
-res_path=config["root"] + "/" + config["resdir"]
###### Target files ######
## raw data stats
diff --git a/workflow/pre-job_snakefiles/Snakefile1.smk b/workflow/pre-job_snakefiles/Snakefile1.smk
index 3314ac7c1b39fb9d80f6f04983765000543cbdb7..da275148fc6061e8d80d99ac93d996247a1b872e 100644
--- a/workflow/pre-job_snakefiles/Snakefile1.smk
+++ b/workflow/pre-job_snakefiles/Snakefile1.smk
@@ -29,6 +29,15 @@ def data_ext(dir, id):
return(str(config["data"] + "/{id}.tar.gz"))
######################## Snakemake ########################
+
+### paths
+if config["root"].startswith("."):
+ abs_root_path = get_abs_root_path()
+ res_path = get_res_path()
+else:
+ abs_root_path = config["root"]
+ res_path = abs_root_path + "/" + config["resdir"]
+
### get filenames for workflow
if config["get_all_tar_filename"]:
IDS=get_tar_name(config["data"])
@@ -36,7 +45,6 @@ else:
IDS=config["tarIDS"]
###### results path ######
-res_path=config["root"] + "/" + config["resdir"]
### target files
rule all:
@@ -60,9 +68,9 @@ rule extract_targz_data:
# move bam and fasta + fastq files
rule move_files:
params:
- root=config["root"],
- bam_path=config["root"] + "/" + config["resdir"] + "/" + config["bamdir"],
- fastx_path=config["root"] + "/" + config["resdir"] + "/" + config["fastxdir"],
+ root=abs_root_path,
+ bam_path=abs_root_path + "/" + config["resdir"] + "/" + config["bamdir"],
+ fastx_path=abs_root_path + "/" + config["resdir"] + "/" + config["fastxdir"],
shell:
"cd {params.root} && "
"mkdir -p {params.bam_path} {params.fastx_path} && "
diff --git a/workflow/pre-job_snakefiles/Snakefile2.smk b/workflow/pre-job_snakefiles/Snakefile2.smk
index b55585c14009c1cf3cc328dac9789a28fcc405b3..1dfcd0d919003c5c2e96af2e2662e34cf50b533f 100644
--- a/workflow/pre-job_snakefiles/Snakefile2.smk
+++ b/workflow/pre-job_snakefiles/Snakefile2.smk
@@ -14,26 +14,34 @@ def get_bams_name(dirpath):
return(IDS)
######################## Snakemake ########################
+
+### root path
+if config["root"].startswith("."):
+ abs_root_path = get_abs_root_path()
+ res_path = get_res_path()
+else:
+ abs_root_path = config["root"]
+ res_path = abs_root_path + "/" + config["resdir"]
+
###### results path ######
-res_path=config["root"] + "/" + config["resdir"]
### get filenames
-IDS=get_bams_name(config["root"] + "/" + config["resdir"] + "/" + config["bamdir"])
+IDS=get_bams_name(abs_root_path + "/" + config["resdir"] + "/" + config["bamdir"])
### target files
rule all:
input:
- expand(config["root"] + "/" + config["resdir"] + "/" + config["fastxdir"] + "/{id}.fastq.gz", id=IDS),
- expand(config["root"] + "/" + config["resdir"] + "/" + config["fastxdir"] + "/{id}.fasta.gz", id=IDS)
+ expand(abs_root_path + "/" + config["resdir"] + "/" + config["fastxdir"] + "/{id}.fastq.gz", id=IDS),
+ expand(abs_root_path + "/" + config["resdir"] + "/" + config["fastxdir"] + "/{id}.fasta.gz", id=IDS)
### rules
## PacBio .bam conversion with smrtlink
# .bam.pbi needed for bam_to_ conversion rules
rule smrtlink_index:
input:
- config["root"] + "/" + config["resdir"] + "/" + config["bamdir"] + "/{id}.bam"
+ abs_root_path + "/" + config["resdir"] + "/" + config["bamdir"] + "/{id}.bam"
output:
- config["root"] + "/" + config["resdir"] + "/" + config["bamdir"] + "/{id}.bam.pbi"
+ abs_root_path + "/" + config["resdir"] + "/" + config["bamdir"] + "/{id}.bam.pbi"
container:
"docker://registry.forgemia.inra.fr/asm4pg/genomasm4pg/smrtlink9.0"
shell:
@@ -42,12 +50,12 @@ rule smrtlink_index:
# convert .bam to .fastq.gz
rule smrtlink_bam_to_fastq:
input:
- bam = config["root"] + "/" + config["resdir"] + "/" + config["bamdir"] + "/{id}.bam",
+ bam = abs_root_path + "/" + config["resdir"] + "/" + config["bamdir"] + "/{id}.bam",
bam_pbi = rules.smrtlink_index.output
output:
- config["root"] + "/" + config["resdir"] + "/" + config["fastxdir"] + "/{id}.fastq.gz"
+ abs_root_path + "/" + config["resdir"] + "/" + config["fastxdir"] + "/{id}.fastq.gz"
params:
- prefix=config["root"] + "/" + config["resdir"] + "/" + config["fastxdir"] + "/{id}"
+ prefix=abs_root_path + "/" + config["resdir"] + "/" + config["fastxdir"] + "/{id}"
priority: 2
container:
"docker://registry.forgemia.inra.fr/asm4pg/genomasm4pg/smrtlink9.0"
@@ -57,12 +65,12 @@ rule smrtlink_bam_to_fastq:
# convert .bam to .fasta.gz
rule smrtlink_bam_to_fasta:
input:
- bam = config["root"] + "/" + config["resdir"] + "/" + config["bamdir"] + "/{id}.bam",
+ bam = abs_root_path + "/" + config["resdir"] + "/" + config["bamdir"] + "/{id}.bam",
bam_pbi = rules.smrtlink_index.output
output:
- config["root"] + "/" + config["resdir"] + "/" + config["fastxdir"] + "/{id}.fasta.gz"
+ abs_root_path + "/" + config["resdir"] + "/" + config["fastxdir"] + "/{id}.fasta.gz"
params:
- prefix=config["root"] + "/" + config["resdir"] + "/" + config["fastxdir"] + "/{id}"
+ prefix=abs_root_path + "/" + config["resdir"] + "/" + config["fastxdir"] + "/{id}"
priority: 2
container:
"docker://registry.forgemia.inra.fr/asm4pg/genomasm4pg/smrtlink9.0"
diff --git a/workflow/pre-job_snakefiles/Snakefile3.smk b/workflow/pre-job_snakefiles/Snakefile3.smk
index d0ab49218d2657c64f5967fe5f23f38f9d13f876..757ab6b0d3e6088301a9b047298a5ae489518932 100644
--- a/workflow/pre-job_snakefiles/Snakefile3.smk
+++ b/workflow/pre-job_snakefiles/Snakefile3.smk
@@ -17,26 +17,33 @@ def get_fastq_name(dirpath):
return(IDS)
######################## Snakemake ########################
+### root path
+if config["root"].startswith("."):
+ abs_root_path = get_abs_root_path()
+ res_path = get_res_path()
+else:
+ abs_root_path = config["root"]
+ res_path = abs_root_path + "/" + config["resdir"]
+
###### results path ######
-res_path=config["root"] + "/" + config["resdir"]
### get filenames
-IDS = get_fastq_name(config["root"] + "/" + config["resdir"] + "/" + config["fastxdir"])
+IDS = get_fastq_name(abs_root_path + "/" + config["resdir"] + "/" + config["fastxdir"])
### target files
rule all:
input:
- expand(config["root"] + "/" + config["resdir"] + "/" + config["fastxdir"] + "/{id}.fasta.gz", id=IDS)
+ expand(abs_root_path + "/" + config["resdir"] + "/" + config["fastxdir"] + "/{id}.fasta.gz", id=IDS)
### rules
# if only fastq : convert to fasta with seqtk + zip
rule convert_to_fasta:
input:
- config["root"] + "/" + config["resdir"] + "/" + config["fastxdir"] + "/{id}.fastq.gz"
+ abs_root_path + "/" + config["resdir"] + "/" + config["fastxdir"] + "/{id}.fastq.gz"
output:
- config["root"] + "/" + config["resdir"] + "/" + config["fastxdir"] + "/{id}.fasta.gz"
+ abs_root_path + "/" + config["resdir"] + "/" + config["fastxdir"] + "/{id}.fasta.gz"
params:
- path=config["root"] + "/" + config["resdir"] + "/" + config["fastxdir"]
+ path=abs_root_path + "/" + config["resdir"] + "/" + config["fastxdir"]
threads: 10
container:
"docker://registry.forgemia.inra.fr/asm4pg/genomasm4pg/seqtk1.3"
diff --git a/workflow/rules/00_runtime.smk b/workflow/rules/00_runtime.smk
index f53da68ef3c9597cc627ecf606bbfaf069224cdc..2c408ba0576d29b43e39a670e8154d2f7285ffa3 100644
--- a/workflow/rules/00_runtime.smk
+++ b/workflow/rules/00_runtime.smk
@@ -28,8 +28,6 @@ rule elasped_time:
with open(output[0], "w") as out:
out.write("Runtime (hh:mm:ss): " + str(td))
- # os.remove(input[0])
-
rule elasped_time_trio:
input:
@@ -49,6 +47,4 @@ rule elasped_time_trio:
td = timedelta(seconds=elapsed_time)
with open(output[0], "w") as out:
- out.write("Runtime (hh:mm:ss): " + str(td))
-
- # os.remove(input[0])
\ No newline at end of file
+ out.write("Runtime (hh:mm:ss): " + str(td))
\ No newline at end of file
diff --git a/workflow/rules/01_qc.smk b/workflow/rules/01_qc.smk
index 8493080eea31c1041b810dab67fcebf1fb453f08..bf963a2f7f96c023b7f95ca54dc8ac6421bedd57 100644
--- a/workflow/rules/01_qc.smk
+++ b/workflow/rules/01_qc.smk
@@ -1,7 +1,7 @@
### QC on .bam files with LongQC
rule longqc:
input:
- config["root"] + "/" + config["resdir"] + "/" + config["bamdir"] + "/{Bid}.bam"
+ abs_root_path + "/" + config["resdir"] + "/" + config["bamdir"] + "/{Bid}.bam"
output:
directory(res_path + "/{Bid}/{run}/01_raw_data_QC/02_longQC")
benchmark:
diff --git a/workflow/rules/02_asm.smk b/workflow/rules/02_asm.smk
index 83c9b2412912b2a02e1cb33d7f21f263214933f1..ee20083a1ea68b2b1a5913d01ba010d1ac8f1280 100644
--- a/workflow/rules/02_asm.smk
+++ b/workflow/rules/02_asm.smk
@@ -5,12 +5,12 @@ rule hifiasm:
input:
get_fasta
output:
- hap1 = config["root"] + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}.bp.hap1.p_ctg.gfa",
- hap2 = config["root"] + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}.bp.hap2.p_ctg.gfa"
+ hap1 = abs_root_path + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}.bp.hap1.p_ctg.gfa",
+ hap2 = abs_root_path + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}.bp.hap2.p_ctg.gfa"
params:
- prefix = config["root"] + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}"
+ prefix = abs_root_path + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}"
benchmark:
- config["root"] + "/" + config["resdir"] + "/{runid}/benchmark/{id}_hifiasm_benchmark.txt"
+ abs_root_path + "/" + config["resdir"] + "/{runid}/benchmark/{id}_hifiasm_benchmark.txt"
threads: 20
resources:
mem_mb=250000
@@ -28,12 +28,12 @@ rule hifiasm_hic:
# hifi reads
hifi = get_fasta
output:
- hap1 = config["root"] + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}.hic.hap1.p_ctg.gfa",
- hap2 = config["root"] + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}.hic.hap2.p_ctg.gfa"
+ hap1 = abs_root_path + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}.hic.hap1.p_ctg.gfa",
+ hap2 = abs_root_path + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}.hic.hap2.p_ctg.gfa"
params:
- prefix= config["root"] + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}"
+ prefix= abs_root_path + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}"
benchmark:
- config["root"] + "/" + config["resdir"] + "/{runid}/benchmark/{id}_hifiasm_hic_benchmark.txt"
+ abs_root_path + "/" + config["resdir"] + "/{runid}/benchmark/{id}_hifiasm_hic_benchmark.txt"
threads: 20
resources:
mem_mb=250000
@@ -48,10 +48,10 @@ rule yak:
p1 = get_p1,
p2 = get_p2
output:
- p1 = config["root"] + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/yak/{id}_parent1.yak",
- p2 = config["root"] + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/yak/{id}_parent2.yak"
+ p1 = abs_root_path + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/yak/{id}_parent1.yak",
+ p2 = abs_root_path + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/yak/{id}_parent2.yak"
benchmark:
- config["root"] + "/" + config["resdir"] + "/{runid}/benchmark/{id}_yak_benchmark.txt"
+ abs_root_path + "/" + config["resdir"] + "/{runid}/benchmark/{id}_yak_benchmark.txt"
container:
"docker://registry.forgemia.inra.fr/asm4pg/genomasm4pg/hifiasm0.16.1"
shell:
@@ -65,12 +65,12 @@ rule hifiasm_trio:
p2 = rules.yak.output.p2,
child = get_fasta
output:
- hap1 = config["root"] + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}.dip.hap1.p_ctg.gfa",
- hap2 = config["root"] + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}.dip.hap2.p_ctg.gfa"
+ hap1 = abs_root_path + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}.dip.hap1.p_ctg.gfa",
+ hap2 = abs_root_path + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}.dip.hap2.p_ctg.gfa"
params:
- prefix = config["root"] + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}"
+ prefix = abs_root_path + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}"
benchmark:
- config["root"] + "/" + config["resdir"] + "/{runid}/benchmark/{id}_hifiasm_trio_benchmark.txt"
+ abs_root_path + "/" + config["resdir"] + "/{runid}/benchmark/{id}_hifiasm_trio_benchmark.txt"
threads: 20
resources:
mem_mb=250000
@@ -88,8 +88,8 @@ rule hap_gfa_to_fasta:
hap1 = get_mode_hap1,
hap2 = get_mode_hap2
output:
- hap1_fa = config["root"] + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}_hap1.fa.gz",
- hap2_fa = config["root"] + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}_hap2.fa.gz"
+ hap1_fa = abs_root_path + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}_hap1.fa.gz",
+ hap2_fa = abs_root_path + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}_hap2.fa.gz"
params:
pigz_p = config["pigz_threads"]
threads: config["pigz_threads"]
diff --git a/workflow/rules/03_asm_qc.smk b/workflow/rules/03_asm_qc.smk
index c3ea246bfac35181459952f898d8fd8e4795f57f..f32a48053ba91a264d687778e061f1eeacdce878 100644
--- a/workflow/rules/03_asm_qc.smk
+++ b/workflow/rules/03_asm_qc.smk
@@ -1,5 +1,5 @@
# input haplotypes
-HAP_FA_GZ = config["root"] + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}_hap{n}.fa.gz"
+HAP_FA_GZ = abs_root_path + "/" + config["resdir"] + "/{runid}/02_genome_assembly/01_raw_assembly/00_assembly/{id}_hap{n}.fa.gz"
# unzip fasta
rule unzip_hap_fasta:
diff --git a/workflow/rules/07_report.smk b/workflow/rules/07_report.smk
index a2321652acc1f979f5f9d9ca5c13b564839457d5..e84bc943dee1cc2b7eb78b786238f4e5a35d59bc 100644
--- a/workflow/rules/07_report.smk
+++ b/workflow/rules/07_report.smk
@@ -1,6 +1,6 @@
### create report at the end of the workflow
+
# path variables
-res_path=config["root"] + "/" + config["resdir"]
RAW_QC = res_path + "/{runid}/01_raw_data_QC"
ASM_QC = res_path + "/{runid}/02_genome_assembly/01_raw_assembly/01_assembly_QC"
P_ASM_QC = res_path + "/{runid}/02_genome_assembly/02_after_purge_dups_assembly/01_assembly_QC"
diff --git a/workflow/scripts/path_helper.py b/workflow/scripts/path_helper.py
new file mode 100644
index 0000000000000000000000000000000000000000..1aa7e2ecf4dc98db435e5fd58883a1c8a730413d
--- /dev/null
+++ b/workflow/scripts/path_helper.py
@@ -0,0 +1,13 @@
+import os
+
+###### root path ######
+def get_abs_root_path():
+ abs_root_path = os.path.abspath(config["root"])
+ return(abs_root_path)
+
+
+###### results path ######
+def get_res_path():
+ abs_root_path = os.path.abspath(config["root"])
+ res_path= abs_root_path + "/" + config["resdir"]
+ return(res_path)
\ No newline at end of file