fix conda

Snakefile

@@ -18,9 +18,9 @@ with open(config['resources'], 'r') as f:
 	resource = yaml.safe_load(f)
 
 ### GET BASENAME FOR READS WILDCARDS ###
-def getBasename4Reads(path):
-	base=os.path.basename(path)
-	return os.path.splitext(base)[0]
+# def getBasename4Reads(path):
+# 	base=os.path.basename(path)
+# 	return os.path.splitext(base)[0]
 
 ### CHECK IF INPUT IS GZIPPED ###
 def gzipped_or_not(path):
@@ -41,14 +41,13 @@ def genomeSize_auto_or_not(given_size):
 	return given_size
 
 
-def addUniqueLibraryID(library):
-	string2Add=library + "_1"
 
-def to_be_smrtTrimmed(userAnswer):
-	if userAnswer == 'True':
-		string2Add="smrtTrimmed"
-	elif userAnswer == 'False':
-		string2Add="notsmrtTrimmed"
+
+	# def to_be_smrtTrimmed(userAnswer):
+	# 	if userAnswer == 'True':
+	# 		string2Add="smrtTrimmed"
+	# 	elif userAnswer == 'False':
+	# 		string2Add="notsmrtTrimmed"
 
 samples = pd.read_csv(config['samplesTSV'], dtype=str, index_col=False, delim_whitespace=True, skip_blank_lines=True)
 if set(['sample', 'Library_R1', 'Library_R2', 'meryl_kmer_size', 'trim10X', 'trimAdapters', 'fastQC']).issubset(samples.columns):

envs/AUXILIARY_PYTHON_SCRIPTS.yaml

@@ -11,3 +11,4 @@ dependencies:
  - pandas
  - numpy
  - ghostscript
+ - python=3.9.*

envs/UNZIP_and_QC.yaml

 channels:
  - anaconda
- - bioconda
  - conda-forge
+ - bioconda
 dependencies:
- - pigz=2.4
- - trim-galore=0.6.6
- - pandoc=2.11
+ - openssl==3.0.5
+ - python=3.10.5=ha86cf86_0_cpython
+ - pigz=2.6
+ - trim-galore=0.6.7
+ - pandoc=2.11.4
  - multiqc=1.9
- - python=3.8.5
  - trimmomatic=0.39

rules/evaluate.smk

@@ -31,7 +31,7 @@ rule unzipFastq_R1_HiC:
 	output:
 		temp(os.path.join(config['Results'], "1_evaluation/{asmID}/HiC_MAPS/{asmID}.HiC.R1.fastq")),
 	log:
-		os.path.join(config['Results'], "1_evaluation/{asmID}/logs/pigzUnzip..HiC.R1.{asmID}.log")
+		os.path.join(config['Results'], "1_evaluation/{asmID}/logs/pigzUnzip.HiC.R1.{asmID}.log")
 	conda:
 		os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
 	threads:
@@ -56,7 +56,7 @@ rule symlink_UnzippedFastq_R1_HiC:
 		None
 	shell:
 		"""
-		ln -s {input} {output}
+		ln -sf {input} {output}
 		"""
 
 
@@ -94,7 +94,7 @@ rule symlink_UnzippedFastq_R2_HiC:
 		None
 	shell:
 		"""
-		ln -s {input} {output}
+		ln -sf {input} {output}
 		"""
 
 
@@ -334,7 +334,7 @@ rule symlink_UnzippedFasta_PRI:
 		None
 	shell:
 		"""
-		ln -s {input} {output}
+		ln -fs {input} {output}
 		"""
 
 ################
@@ -350,7 +350,7 @@ rule unzipFasta_ALT:
 	log:
 		os.path.join(config['Results'], "1_evaluation/{asmID}/logs/pigzUnzip.ALT.{asmID}.log")
 	conda:
-		os.path.join(workflow.basedir, "envs/pigz.yaml")
+		os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
 	threads:
 		resource['unzipFasta_ALT']['threads']
 	resources:
@@ -431,7 +431,7 @@ rule merqury:
 		os.path.join(workflow.basedir, "envs/MERYL_MERQURY.yaml")
 	shell:
 		"""
-		ln -s {input.merylDB_provided} {params.symlink_merylDB}
+		ln -fs {input.merylDB_provided} {params.symlink_merylDB}
 		cd {params.outPath}
 		export OMP_NUM_THREADS={threads}
 		(merqury.sh {params.symlink_merylDB} {input.assemblyPRI} {input.assemblyALT} {params.outFile}) &> {log}