Merge branch 'devel' into master_new

bioinfo-core-BGU · Jun 26, 2019 · 0ce2308 · 0ce2308
2 parents 895968b + cc454e1
commit 0ce2308
Show file tree

Hide file tree

Showing 49 changed files with 3,509 additions and 898 deletions.
diff --git a/Workflows/Assembly_Indexing_mapping.yaml b/Workflows/Assembly_Indexing_mapping.yaml
@@ -29,7 +29,7 @@ Vars:
         trimmo:             /path/to/trimmomatic
 Step_params:
     merge1:
-        module:             merge
+        module:   Import
         script_path:        {Vars.paths.merge}
     fqc_merge1:
         module:             fastqc_html

diff --git a/Workflows/BLAST_db.yaml b/Workflows/BLAST_db.yaml
@@ -35,7 +35,7 @@ Vars:
             table:      /path/to/uniprot_sprot.tsv
 Step_params:
     merge_nucl:
-        module:             merge
+        module:   Import
         script_path:        {Vars.paths.merge}
 ############################ 1. BLAST db construction
     mkblst_nucl:

diff --git a/Workflows/BLAST_fasta.yaml b/Workflows/BLAST_fasta.yaml
@@ -45,7 +45,7 @@ Vars:
 Step_params:
 ############################ 1. merge and QC
     merge_reads:
-        module:             merge
+        module:   Import
         script_path:        {Vars.paths.merge}
     fqc_merge:
         module:             fastqc_html

diff --git a/Workflows/BLAST_test.yaml b/Workflows/BLAST_test.yaml
@@ -31,7 +31,7 @@ Vars:
 Step_params:
 ############################ 1. merge and QC
     Merge_smp:
-        module:             merge
+        module:   Import
         script_path:        {Vars.paths.merge}
         src:                [Nucleotide, Protein, BED]
         trg:                [null,null   ,bed]
@@ -41,7 +41,7 @@ Step_params:
 
 
     Merge_prj:
-        module:             merge
+        module:   Import
         script_path:        {Vars.paths.merge}
         src:                [Nucleotide, Protein, BED]
         trg:                [null,null   ,bed]

diff --git a/Workflows/Basic_Preparation.yaml b/Workflows/Basic_Preparation.yaml
@@ -38,13 +38,13 @@ Vars:
 Step_params:
 # ---------------------------------- 1. Merge, QC  and trimming
     merge1:
-        module:         merge
-        script_path:    
+        module:   Import
+        script_path:
         intermediate:
         tag:            basic
-
+        
     merge_advanced:
-        module:         merge
+        module:   Import
         src:
             - Forward
             - Reverse
@@ -85,6 +85,7 @@ Step_params:
             --tag:
             --force: 
             --threads:  10
+        export:
 
     fastq_screen_alt2:
         module:         fastq_screen

diff --git a/Workflows/ChIP_seq.yaml b/Workflows/ChIP_seq.yaml
@@ -55,8 +55,8 @@ Vars:
 Step_params:
 # ---------------------------------- 1. Merge, QC  and trimming
     merge1:
-        module:         merge
-        script_path:    
+        module:   Import
+        script_path:
         tag:            QC
     fqc_merge1:
         module:         fastqc_html

diff --git a/Workflows/Clustering.yaml b/Workflows/Clustering.yaml
@@ -23,8 +23,9 @@ Description: |
 
 Step_params:
     merge1:
-        module:         merge
+        module:   Import
         script_path:    {Vars.paths.merge}
+        # stop_and_show:
     derepel1:
         module:         vsearch_derepel
         base:           merge1

diff --git a/Workflows/Example_WF_from_ftp.yaml b/Workflows/Example_WF_from_ftp.yaml
@@ -48,7 +48,7 @@ Vars:
 Step_params:
 
     Merge:
-        module:         merge 
+        module:    Import
         script_path:    echo -n   
         pipe:           xargs -0 -d " " curl | gzip -cd 
         redirects:

diff --git a/Workflows/GATK_workflow.yaml b/Workflows/GATK_workflow.yaml
@@ -21,7 +21,7 @@ Vars:
         VEP_cache:          /path/to/VEP/ensembl-vep-release-88.10/cache
 Step_params:
     Merge:
-        module: merge
+        module:   Import
         script_path: gzip -cd
     Trimmomatic:
         module: trimmo

diff --git a/Workflows/Metagenomics.yaml b/Workflows/Metagenomics.yaml
@@ -98,7 +98,7 @@ Step_params:
     ##Preprocessing
 
     Merge:        
-        module:         merge
+        module:   Import
         script_path:
 
     Trim_Galore:

diff --git a/Workflows/Microbe-Flow/Microbe-Flow.yaml b/Workflows/Microbe-Flow/Microbe-Flow.yaml
@@ -84,8 +84,8 @@ Vars:
 Step_params:
 
     Merge:
-        module: merge
-        script_path: 
+        module:   Import
+        script_path:
 
     FastQC_Merge:
         module: fastqc_html
@@ -201,6 +201,7 @@ Step_params:
         module: Prokka
         base: Spades
         script_path: {Vars.Programs_path.Prokka}
+        scope:          sample
         qsub_params:
             -pe: '{Vars.Parallel_Environment.pe_name}  {Vars.Parallel_Environment.Prokka}'
         generate_GFF_dir: null

diff --git a/Workflows/Microbe-Flow/Microbe-Flow_conda.yaml b/Workflows/Microbe-Flow/Microbe-Flow_conda.yaml
@@ -97,8 +97,8 @@ Vars:
 Step_params:
 
     Merge:
-        module: merge
-        script_path: 
+        module:   Import
+        script_path:
 
     FastQC_Merge:
         module: fastqc_html
@@ -214,6 +214,7 @@ Step_params:
         module: Prokka
         base: Spades
         script_path: {Vars.Programs_path.Prokka}
+        scope:          sample
         qsub_params:
             -pe: '{Vars.Parallel_Environment.pe_name}  {Vars.Parallel_Environment.Prokka}'
         generate_GFF_dir: null

diff --git a/Workflows/Microbe-Flow/Microbe-Flow_conda_test_run.yaml b/Workflows/Microbe-Flow/Microbe-Flow_conda_test_run.yaml
@@ -86,7 +86,7 @@ Vars:
 Step_params:
 
     Merge:
-        module:         merge 
+        module:    Import
         script_path:    curl 
         pipe:           gzip  -cd 
         redirects:

diff --git a/Workflows/QIIME2_MovingPic.yaml b/Workflows/QIIME2_MovingPic.yaml
@@ -17,7 +17,7 @@ Step_params:
     # 2. metadata is imported using 'cat' 
     # 3. TaxonomicClassifier is imported with curl -L, because it is a remote file
     merge_data:
-        module:         merge
+        module:   Import
         src:            [EMPSingleEndSequences, metadata, TaxonomicClassifier]
         trg:            [EMPSingleEndSequences, metadata, TaxonomicClassifier]
         script_path:    [..import.., cat, 'curl -L']

diff --git a/Workflows/RNASeq_Bowtie2.yaml b/Workflows/RNASeq_Bowtie2.yaml
@@ -44,8 +44,8 @@ Vars:
     min_quality: '25'
 Step_params:
   Merge:
-    module: merge
-    script_path: 
+    module:   Import
+   script_path:
   FastQC_Merge:
     base: Merge
     module: fastqc_html

diff --git a/Workflows/RNASeq_STAR.yaml b/Workflows/RNASeq_STAR.yaml
@@ -44,8 +44,8 @@ Vars:
     min_quality: '25'
 Step_params:
   Merge:
-    module: merge
-    script_path: 
+    module:   Import
+   script_path:
   FastQC_Merge:
     base: Merge
     module: fastqc_html

diff --git a/Workflows/RNA_seq_Trinity.yaml b/Workflows/RNA_seq_Trinity.yaml
@@ -64,6 +64,7 @@ Vars:
         fastqc:             fastqc
         trimmomatic:        trimmomatic
         Trinity:            Trinity
+        TrinityStats:       TrinityStats.pl
         get_Trinity_gene_to_trans_map: get_Trinity_gene_to_trans_map.pl
         trinity_scripts:    ""
         BUSCO:              run_BUSCO.py
@@ -92,7 +93,7 @@ Step_params:
     # -------------------- Part 1: Merging and QC
     # Copy and concatenate files into data directory:
     Merge:
-        module:             merge
+        module:   Import
         script_path:
         tag:                QC
     # FastQC on the files
@@ -159,6 +160,9 @@ Step_params:
             --max_memory:       10G
             --SS_lib_type:      RF
             # --full_cleanup:
+        TrinityStats:
+            path:           {Vars.paths.TrinityStats}
+
         # stop_and_show:
 
     # Map the reads to the assembly

diff --git a/Workflows/RNA_seq_reference.yaml b/Workflows/RNA_seq_reference.yaml
@@ -32,7 +32,7 @@ Vars:
         STAR_index:         /path/to/GRCh38_STARind/            # Directory in which STAR index was created
 Step_params:
     merge1:
-        module:             merge
+        module:   Import
         script_path:        {Vars.paths.merge}
     trim1:
         module:             trimmo

diff --git a/Workflows/RSEM.yaml b/Workflows/RSEM.yaml
@@ -24,7 +24,7 @@ Vars:
 Step_params:
 # ---------------------------------- 1. Merge, QC  and trimming
     merge1:
-        module:         merge
+        module:   Import
         script_path:    #{Vars.paths.merge}
         # stop_and_show:
 

diff --git a/Workflows/filtering_by_mapping.yaml b/Workflows/filtering_by_mapping.yaml
@@ -46,7 +46,7 @@ Vars:
 Step_params:
 # ---------------------------------- 1. Merge, QC  and trimming
     merge1:
-        module:         merge
+        module:   Import
         script_path:    {Vars.paths.merge}
     fqc_merge1:
         module:         fastqc_html

diff --git a/Workflows/parameter_set_QIIME/QIIME_workflow.yaml b/Workflows/parameter_set_QIIME/QIIME_workflow.yaml
@@ -55,7 +55,7 @@ Vars:
         id_to_taxonomy:     /path/to/majority_taxonomy_7_levels.txt
 Step_params:
     merge1:                            
-        module:             merge
+        module:   Import
         script_path:        {Vars.paths.merge}
     fQC_merge:
         module:             fastqc_html

diff --git a/Workflows/project_merge.yaml b/Workflows/project_merge.yaml
@@ -7,15 +7,15 @@ Global_params:
 
 Step_params:
     merge_proj:
-        module:             merge
+        module:   Import
         script_path:        [cat,     cat ]
         src:                [TYP1,    TYP2]
         trg:                [typ1,    typ2]
         ext:                typ
         scope:              project
 
     merge_smp:
-        module:             merge
+        module:   Import
         script_path:        # Guess
         src:                [Forward, Reverse]
         trg:                [null,    null   ]