correct path, change rules names

tdayris · Feb 19, 2024 · 47d0d17 · 47d0d17
1 parent a717168
commit 47d0d17
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Showing 7 changed files with 22 additions and 14 deletions.
diff --git a/bigr_pipelines/global_qc/Snakefile b/bigr_pipelines/global_qc/Snakefile
@@ -13,7 +13,7 @@ onstart:
 
 ############################
 ### Get data information ###
-############################
+############################da
 
 
 include: "rules/000.common.smk"
@@ -116,13 +116,21 @@ if os.path.isfile(supplementary_design):
                         dic_DATA[i][j][k]['Library_Name']=sub_sub_sub_data.Library_Name.values.tolist()
                         dic_DATA[i][j][k]['Species']=''.join(set(sub_sub_sub_data.Species)) #''.join() allow to convert set() type in string.
                         #get path of fastq files for this sample
-                        dic_DATA[i][j][k]['Fastq_Files'] = [ os.path.abspath(l) for l in sum([ glob.glob('./data_input/**/' + l +'_S[0-9]*_R[1-3]_*.f*q.gz',  recursive=True) for l in dic_DATA[i][j][k]['Library_Name']], [])]
+                        dic_DATA[i][j][k]['Fastq_Files'] = [ os.path.abspath(l) for l in sum([ glob.glob('./*input/**/' + l +'_S[0-9]*_R[1-3]_*.f*q.gz',  recursive=True) for l in dic_DATA[i][j][k]['Library_Name']], [])]
                         #print("Library : " + k)
                         #print("Library Name : " + ",".join(dic_DATA[i][j][k]['Library_Name']))
                         #print("Species : " + dic_DATA[i][j][k]['Species'])
                         #print("Fastq Files : " + ",".join(dic_DATA[i][j][k]['Fastq_Files']) + "\n")
 
 
+################################
+### Get pipeline information ###
+################################
+
+
+PIPELINE_FOLDER = workflow.snakefile
+PIPELINE_FOLDER = PIPELINE_FOLDER.replace("/Snakefile", "")
+
 
 ##################################
 ### Gather all quality reports ###
@@ -172,7 +180,7 @@ else:
 
 
 if isScRNAData:
-    include: "rules/007.cellranger_csv_RNA.smk"
+    include: "rules/007.csv_cellranger_multi_RNA.smk"
     include: "rules/008.cellranger_multi_RNA.smk"
     include: "rules/009.concat_cellranger_multi_RNA.smk"
 
@@ -183,7 +191,7 @@ if isScATACData:
 
 
 if isScRNAATACData:
-    include: "rules/007.cellranger_csv_RNA_ATAC.smk"
+    include: "rules/007.csv_cellranger_arc_RNA_ATAC.smk"
     include: "rules/008.cellranger_arc_RNA_ATAC.smk"
     include: "rules/009.concat_cellranger_arc_RNA_ATAC.smk"
 

diff --git a/..._qc/rules/007.cellranger_csv_RNA_ATAC.smk → ...rules/007.csv_cellranger_arc_RNA_ATAC.smk b/..._qc/rules/007.cellranger_csv_RNA_ATAC.smk → ...rules/007.csv_cellranger_arc_RNA_ATAC.smk
@@ -1,6 +1,6 @@
 # Make csv config file for CellRanger
 """
-007.cellranger_csv
+007.csv_cellranger_arc_RNA_ATAC
 from
 -> Entry job
 by

diff --git a/...lobal_qc/rules/007.cellranger_csv_RNA.smk → ...qc/rules/007.csv_cellranger_multi_RNA.smk b/...lobal_qc/rules/007.cellranger_csv_RNA.smk → ...qc/rules/007.csv_cellranger_multi_RNA.smk
diff --git a/bigr_pipelines/global_qc/rules/008.cellranger_arc_RNA_ATAC.smk b/bigr_pipelines/global_qc/rules/008.cellranger_arc_RNA_ATAC.smk
@@ -2,7 +2,7 @@
 """
 008.cellranger_arc_RNA_ATAC
 from
--> 007.cellranger_csv_RNA_ATAC
+-> 007.csv_cellranger_arc_RNA_ATAC
 by
 -> 003.multiqc
 -> 003.irods_complient
@@ -47,4 +47,4 @@ rule cellranger_arc:
     log:
         "logs/cellranger/{CR_sample}_cellranger_arc.log"
     shell:
-        "module load singularity/3.6.3 && singularity exec --no-home {params.sing_arg} ../envs/cellranger_arc_v2.0.2.simg ../scripts/script_cellranger_arc_RNA_ATAC.sh {threads} {resources.mem_mb} {wildcards.CR_sample} {params.csv_config} {params.reference} $(pwd)"
+        "module load singularity/3.6.3 && singularity exec --no-home {params.sing_arg} -B {PIPELINE_FOLDER}/scripts/:{PIPELINE_FOLDER}/scripts/ {PIPELINE_FOLDER}/envs/cellranger_arc_v2.0.2.simg {PIPELINE_FOLDER}/scripts/script_cellranger_arc_RNA_ATAC.sh {threads} {resources.mem_mb} {wildcards.CR_sample} {params.csv_config} {params.reference} $(pwd)"
diff --git a/bigr_pipelines/global_qc/rules/008.cellranger_atac_ATAC.smk b/bigr_pipelines/global_qc/rules/008.cellranger_atac_ATAC.smk
@@ -1,6 +1,6 @@
 # Run CellRanger
 """
-008.cellranger_atac
+008.cellranger_atac_ATAC
 from
 -> Entry job
 by
@@ -53,4 +53,4 @@ rule cellranger_atac:
     log:
         "logs/cellranger/{CR_sample}_cellranger_atac.log"
     shell:
-        "module load singularity/3.6.3 && singularity exec --no-home {params.sing_arg} ../envs/cellranger_atac_v2.1.0.simg ../scripts/script_cellranger_atac_ATAC.sh {threads} {resources.mem_mb} {wildcards.CR_sample} {params.library_names} {params.reference} {params.path_fastqs} $(pwd)"
+        "module load singularity/3.6.3 && singularity exec --no-home {params.sing_arg} -B {PIPELINE_FOLDER}/scripts/:{PIPELINE_FOLDER}/scripts/ {PIPELINE_FOLDER}/envs/cellranger_atac_v2.1.0.simg {PIPELINE_FOLDER}/scripts/script_cellranger_atac_ATAC.sh {threads} {resources.mem_mb} {wildcards.CR_sample} {params.library_names} {params.reference} {params.path_fastqs} $(pwd)"
diff --git a/bigr_pipelines/global_qc/rules/008.cellranger_multi_RNA.smk b/bigr_pipelines/global_qc/rules/008.cellranger_multi_RNA.smk
@@ -1,8 +1,8 @@
 # Run CellRanger
 """
-008.cellranger_multi
+008.cellranger_multi_RNA
 from
--> 007.cellranger_csv_RNA
+-> 007.csv_cellranger_multi_RNA
 by
 -> 003.multiqc
 -> 003.irods_complient
@@ -37,4 +37,4 @@ rule cellranger_multi:
     log:
         "logs/cellranger/{CR_sample}_cellranger_multi.log"
     shell:
-        "module load singularity/3.6.3 && singularity exec --no-home {params.sing_arg} ../envs/cellranger_v7.2.0.simg ../scripts/script_cellranger_multi_RNA_TCR_BCR.sh {threads} {resources.mem_mb} {wildcards.CR_sample} {params.csv_config} $(pwd)"
+        "module load singularity/3.6.3 && singularity exec --no-home {params.sing_arg} -B {PIPELINE_FOLDER}/scripts/:{PIPELINE_FOLDER}/scripts/  {PIPELINE_FOLDER}/envs/cellranger_v7.2.0.simg {PIPELINE_FOLDER}/scripts/script_cellranger_multi_RNA_TCR_BCR.sh {threads} {resources.mem_mb} {wildcards.CR_sample} {params.csv_config} $(pwd)"
diff --git a/bigr_pipelines/global_qc/rules/009.concat_cellranger_multi_RNA.smk b/bigr_pipelines/global_qc/rules/009.concat_cellranger_multi_RNA.smk
@@ -26,7 +26,7 @@ rule concat_cellranger_multi:
     output:
         concat_multi=temp("cellranger/csv_concat/CellRanger_RNA_summary_mqc.csv")
     message:
-        "Computing concatenation of CelleRanger multi metrics_summary.csv files"
+        "Computing concatenation of CellRanger multi metrics_summary.csv files"
     threads: 1
     resources:
         mem_mb=lambda wildcard, attempt: attempt * 1000,
@@ -77,7 +77,7 @@ rule concat_cellranger_multi:
         final_df.columns = [w.replace('"', '') for w in final_df.columns]
 
         #sauvegarder le df en format csv
-        final_df.to_csv(output.concat_multi, sep=',',header=True, index=False, na_rep='0', decimal='.')
+        final_df.to_csv(output.concat_multi, sep=',',header=True, index=False, na_rep='NA', decimal='.')