diff --git a/config/config.yaml b/config/config.yaml
index c7a3476f68a2d5baa06dbdc3fe5eea4be9f9a75b..ea03c216342e4feaf862ee86f2eb84b3a32ca402 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -1,91 +1,55 @@
---
-#### GLOBAL PARAMETERS #####
-
-# Directories
-# Usually there is no need to change these
-samples: "test_files/samples_table.csv" # For the mapping worflow
-quantify_input_dir: "results" # For the quantify worflow
-output_dir: "results"
-scripts_dir: "../scripts"
-local_log: "logs/local"
-cluster_log: "logs/cluster"
-
-#######################################################################################################
-####
-#### PREPARE PARAMETERS
-####
-#######################################################################################################
-
-# Isomirs annotation
-# Number of base pairs to add/substract from 5' (start) and 3' (end) coordinates.
-bp_5p: [-1, 0, +1]
-bp_3p: [-1, 0, +1]
-
-
-#### PARAMETERS SPECIFIC TO INPUTS #####
-
-organism: "homo_sapiens/chrY"
-
-homo_sapiens/chrY:
- # URLs to genome, gene & miRNA annotations
- genome_url: "ftp://ftp.ensembl.org/pub/release-98/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.Y.fa.gz"
- gtf_url: "ftp://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/Homo_sapiens.GRCh38.98.gtf.gz"
- mirna_url: "https://www.mirbase.org/ftp/CURRENT/genomes/hsa.gff3"
-
- # Chromosome name mappings between UCSC <-> Ensembl
- # Other organisms available at: https://github.com/dpryan79/ChromosomeMappings
- map_chr_url: "https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/GRCh38_UCSC2ensembl.txt"
- # Chromosome name mapping parameters:
- column: 1
- delimiter: "TAB"
-
-#######################################################################################################
-####
-#### MAP PARAMETERS
-####
-#######################################################################################################
-
-#### PARAMETERS SPECIFIC TO INPUTS #####
-
-# All of these are produced by the "prepare" workflow
-genome: "results/homo_sapiens/chrY/genome.processed.fa"
-gtf: "results/homo_sapiens/chrY/gene_annotations.filtered.gtf"
-transcriptome: "results/homo_sapiens/chrY/transcriptome_idtrim.fa"
-transcriptome_index_segemehl: "results/homo_sapiens/chrY/transcriptome_index_segemehl.idx"
-genome_index_segemehl: "results/homo_sapiens/chrY/genome_index_segemehl.idx"
-exons: "results/homo_sapiens/chrY/exons.bed"
-header_of_collapsed_fasta: "results/homo_sapiens/chrY/headerOfCollapsedFasta.sam"
-
-
-#### TOOL PARAMETERS ####
+#############################
+#### REQUIRED PARAMETERS ####
+#############################
+
+samples: test_files/samples_table.csv
+
+#### GENOME RESOURCES ####
+
+
+genome_url: "ftp://ftp.ensembl.org/pub/release-98/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.Y.fa.gz"
+gtf_url: "ftp://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/Homo_sapiens.GRCh38.98.gtf.gz"
+mirna_url: "https://www.mirbase.org/ftp/CURRENT/genomes/hsa.gff3"
+map_chr_url: "https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/GRCh38_UCSC2ensembl.txt"
+
+
+
+###############################
+#### "OPTIONAL" PARAMETERS ####
+###############################
+
+#### DIRECTORIES #####
+
+output_dir: results/
+local_log: logs/local/
+cluster_log: logs/cluster/
+scripts_dir: ../scripts/
+
+
+#### ISOMIR GENERATION PARAMETERS ####
+
+bp_5p: [-2, -1, 0, +1, +2]
+bp_3p: [-2, -1, 0, +1, +2]
+
+
+#### PROCESSING PARAMETERS ####
# quality filter
-q_value: 10
-p_value: 50
+q_value: 10
+p_value: 50
# adapter removal
-error_rate: 0.1
-minimum_length: 15
-overlap: 3
-max_n: 0
+error_rate: 0.1
+minimum_length: 15
+overlap: 3
+max_n: 0
# mapping
-max_length_reads: 30
-nh: 100
+max_length_reads: 30
+nh: 100
-#######################################################################################################
-####
-#### QUANTIFY PARAMETERS
-####
-#######################################################################################################
+#### QUANTIFICATION PARAMETERS ####
-
-# Types of miRNAs to quantify
-#mir_list: ["miRNA", "miRNA_primary_transcript", "isomirs"]
mir_list: ["miRNA", "miRNA_primary_transcript"]
-
-# Resources: miR annotations, chromosome name mappings
-# All of these are produced by the "prepare" workflow
-mirnas_anno: "results/homo_sapiens/chrY/mirna_filtered.bed"
-isomirs_anno: "results/homo_sapiens/chrY/isomirs_annotation.bed"
...
\ No newline at end of file
diff --git a/config/config_template.yaml b/config/config_template.yaml
index 62b061a4df558f67d29dad5a1a878d1dfa083456..0a2afb77a20aa920270a716f08bc50f70011370f 100644
--- a/config/config_template.yaml
+++ b/config/config_template.yaml
@@ -1,98 +1,84 @@
---
-#### GLOBAL PARAMETERS #####
-
-# Directories
-# Usually there is no need to change these
-samples: "test_files/samples_table.csv" # For the mapping worflow
-quantify_input_dir: "results" # For the quantify worflow
-output_dir: "results"
-scripts_dir: "../scripts"
-local_log: "logs/local"
-cluster_log: "logs/cluster"
-#######################################################################################################
-####
-#### PREPARE PARAMETERS
-####
-#######################################################################################################
-
-# Isomirs annotation file
-# Number of base pairs to add/substract from 5' (start) and 3' (end) coordinates.
-bp_5p: [0] # array of numbers, e.g., [-2,-1,0,+1], to include 2 upstream and 1 downstream nts
-bp_3p: [0] # array of numbers, e.g., [-2,-1,0,+1], to include 2 upstream and 1 downstream nts
-
-
-#### PARAMETERS SPECIFIC TO INPUTS #####
-
-organism: "org/pre" # e.g., "homo_sapiens/GRCh38.100" or "mus_musculus/GRCm37.98"
-# this string specifies a path, and the "/" is important for this
-# "pre" specifies the assembly version
-
-
-org/pre: # One section for each list item in "organism"; entry should match precisely what
-# is in the "organism" section above, one entry per list item above, omitting the ""
- # URLs to genome, gene & miRNA annotations
- genome_url: # FTP/HTTP URL to gzipped genome in FASTA format, Ensembl style
- # e.g. "ftp://ftp.ensembl.org/pub/release-106/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz"
- gtf_url: # FTP/HTTP URL to gzipped gene annotations in GTF format, Ensembl style
- # e.g. "ftp://ftp.ensembl.org/pub/release-106/gtf/homo_sapiens/Homo_sapiens.GRCh38.106.chr.gtf.gz"
- mirna_url: # FTP/HTTP URL to unzipped microRNA annotations in GFF format, miRBase style
- # e.g. "https://www.mirbase.org/ftp/CURRENT/genomes/hsa.gff3"
-
- # Chromosome name mappings between UCSC <-> Ensembl
- # Other organisms available at: https://github.com/dpryan79/ChromosomeMappings
- map_chr_url: # FTP/HTTP URL to mapping table
- # e.g. "https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/GRCh38_UCSC2ensembl.txt"
- # Chromosome name mapping parameters:
- column: 1 # Column number from input file where to change chromosome name
- delimiter: "TAB" # Delimiter of the input file
-
-#######################################################################################################
-####
-#### MAP PARAMETERS
-####
-#######################################################################################################
-
-#### PARAMETERS SPECIFIC TO INPUTS #####
-
-# Resources: genome, transcriptome, genes, miRs
-# All of these are produced by the "prepare" workflow
-genome: "path/to/genome.processed.fa"
-gtf: "path/to/gene_annotations.filtered.gtf"
-transcriptome: "path/to/transcriptome_idtrim.fa"
-transcriptome_index_segemehl: "path/to/transcriptome_index_segemehl.idx"
-genome_index_segemehl: "path/to/genome_index_segemehl.idx"
-exons: "path/to/exons.bed"
-header_of_collapsed_fasta: "path/to/headerOfCollapsedFasta.sam"
-
-#### TOOL PARAMETERS ####
+#############################
+#### REQUIRED PARAMETERS ####
+#############################
+
+# All paths are relative to the current working directory unless noted otherwise
+
+samples: path/to/samples_table.csv
+
+#### GENOME RESOURCES #####
+
+# All genome resources have to match the source/organism
+# of all samples in the sample table
+
+# FTP/HTTP URL to gzipped genome in FASTA format, Ensembl style
+genome_url: # e.g. "ftp://ftp.ensembl.org/pub/release-106/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz"
+
+# FTP/HTTP URL to gzipped gene annotations in GTF format, Ensembl style
+gtf_url: # e.g. "ftp://ftp.ensembl.org/pub/release-106/gtf/homo_sapiens/Homo_sapiens.GRCh38.106.chr.gtf.gz"
+
+# FTP/HTTP URL to unzipped microRNA annotations in GFF format, miRBase style
+mirna_url: # e.g. "https://www.mirbase.org/ftp/CURRENT/genomes/hsa.gff3"
+
+# Tab-separated mappings table between UCSC (column 1)
+# and Ensembl (coulm 2) chromosome names
+# Available at: https://github.com/dpryan79/ChromosomeMappings
+map_chr_url: # e.g. "https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/GRCh38_UCSC2ensembl.txt"
+
+
+###############################
+#### "OPTIONAL" PARAMETERS ####
+###############################
+
+# The below parameters only need to be changed if the default behavior of
+# MIRFLOWZ is to be changed; however, they still need to be present!
+
+#### DIRECTORIES ####
+
+output_dir: results/
+local_log: logs/local/
+cluster_log: logs/cluster/
+scripts_dir: ../scripts/
+
+
+#### ISOMIR GENERATION PARAMETERS ####
+
+# Generate isomiR annotations with the indicated number of shifts relative to
+# the start and end position of each annotated mature miRNA, as an array of
+# relative positions
+# Examples:
+# - `bp_5p: [-2,0,+1]` and `bp_3p: [+1]` generates 3 isomiRs for each mature
+# miRNA: one that starts two nucleotides before, one that starts exactly at
+# and one that starts one nucleotide after the annotated mature miRNA; all
+# isomiRs will stop one nucleotide after the end of the annotated mature
+# miRNA; note that because `0` is not included in the `bp_3p` array, the
+# annotated mature miRNAs will not be included in this example
+# - Use `bp_5p: [0]` and `bp_3p: [0]` to only include the mature annotated
+# miRNAs and no isomiRs
+
+bp_5p: [-2, -1, 0, +1, +2]
+bp_3p: [-2, -1, 0, +1, +2]
+
+#### PROCESSING PARAMETERS ####
# quality filter
q_value: 10 # Q (Phred) score; minimum quality score to keep
p_value: 50 # minimum % of bases that must have Q quality
# adapter removal
-error_rate: 0.1 # fraction of allowed errors
+error_rate: 0.1 # fraction of allowed errors
minimum_length: 15 # discard processed reads shorter than the indicated length
-overlap: 3 # minimum overlap length of adapter and read to trim the bases
-max_n: 0 # discard reads containing more than the indicated number of N bases
+overlap: 3 # minimum overlap length of adapter and read to trim the bases
+max_n: 0 # discard reads containing more than the indicated number of N bases
# mapping
max_length_reads: 30 # maximum length of processed reads to map with oligomap
-nh: 100 # discard reads with more mappings than the indicated number
-
-#######################################################################################################
-####
-#### QUANTIFY PARAMETERS
-####
-#######################################################################################################
+nh: 100 # discard reads with more mappings than the indicated number
+#### QUANTIFICATION PARAMETERS ####
# Types of miRNAs to quantify
# Remove miRNA types you are not interested in
mir_list: ["miRNA", "miRNA_primary_transcript", "isomirs"]
-
-# Resources: miR annotations, chromosome name mappings
-# All of these are produced by the "prepare" workflow
-mirnas_anno: "path/to/mirna_filtered.bed"
-isomirs_anno: "path/to/isomirs_annotation.bed"
-...
\ No newline at end of file
+...
diff --git a/test/config.yaml b/test/config.yaml
index c5e23a221a244c731142db7fe29cb508cd75bbad..9308d853d0a6cdf0cc9cefc91034087017e9a726 100644
--- a/test/config.yaml
+++ b/test/config.yaml
@@ -1,90 +1,53 @@
---
-#### GLOBAL PARAMETERS #####
+#############################
+#### REQUIRED PARAMETERS ####
+#############################
-# Directories
-# Usually there is no need to change these
-samples: "test_files/samples_table.csv" # For the mapping worflow
-quantify_input_dir: "results" # For the quantify worflow
-output_dir: "results"
-scripts_dir: "../scripts"
-local_log: "logs/local"
-cluster_log: "logs/cluster"
+samples: test_files/samples_table.csv
-#######################################################################################################
-####
-#### PREPARE PARAMETERS
-####
-#######################################################################################################
+#### GENOME RESOURCES ####
-# Isomirs annotation
-# Number of base pairs to add/substract from 5' (start) and 3' (end) coordinates.
-bp_5p: [-1, 0, +1]
-bp_3p: [-1, 0, +1]
+genome_url: "ftp://ftp.ensembl.org/pub/release-98/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.Y.fa.gz"
+gtf_url: "ftp://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/Homo_sapiens.GRCh38.98.gtf.gz"
+mirna_url: "https://www.mirbase.org/ftp/CURRENT/genomes/hsa.gff3"
+map_chr_url: "https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/GRCh38_UCSC2ensembl.txt"
-#### PARAMETERS SPECIFIC TO INPUTS #####
+###############################
+#### "OPTIONAL" PARAMETERS ####
+###############################
-organism: "homo_sapiens/chrY"
+#### DIRECTORIES #####
-homo_sapiens/chrY:
- # URLs to genome, gene & miRNA annotations
- genome_url: "ftp://ftp.ensembl.org/pub/release-98/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.Y.fa.gz"
- gtf_url: "ftp://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/Homo_sapiens.GRCh38.98.gtf.gz"
- mirna_url: "https://www.mirbase.org/ftp/CURRENT/genomes/hsa.gff3"
+output_dir: results/
+local_log: logs/local/
+cluster_log: logs/cluster/
+scripts_dir: ../scripts/
- # Chromosome name mappings between UCSC <-> Ensembl
- # Other organisms available at: https://github.com/dpryan79/ChromosomeMappings
- map_chr_url: "https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/GRCh38_UCSC2ensembl.txt"
- # Chromosome name mapping parameters:
- column: 1
- delimiter: "TAB"
-#######################################################################################################
-####
-#### MAP PARAMETERS
-####
-#######################################################################################################
+#### ISOMIR GENERATION PARAMETERS ####
-#### PARAMETERS SPECIFIC TO INPUTS #####
+bp_5p: [-2, -1, 0, +1, +2]
+bp_3p: [-2, -1, 0, +1, +2]
-genome: "results/homo_sapiens/chrY/genome.processed.fa"
-gtf: "results/homo_sapiens/chrY/gene_annotations.filtered.gtf"
-transcriptome: "results/homo_sapiens/chrY/transcriptome_idtrim.fa"
-transcriptome_index_segemehl: "results/homo_sapiens/chrY/transcriptome_index_segemehl.idx"
-genome_index_segemehl: "results/homo_sapiens/chrY/genome_index_segemehl.idx"
-exons: "results/homo_sapiens/chrY/exons.bed"
-header_of_collapsed_fasta: "results/homo_sapiens/chrY/headerOfCollapsedFasta.sam"
-
-#### TOOL PARAMETERS ####
+#### PROCESSING PARAMETERS ####
# quality filter
-q_value: 10
-p_value: 50
+q_value: 10
+p_value: 50
# adapter removal
-error_rate: 0.1
-minimum_length: 15
-overlap: 3
-max_n: 0
+error_rate: 0.1
+minimum_length: 15
+overlap: 3
+max_n: 0
# mapping
-max_length_reads: 30
-nh: 100
-
-#######################################################################################################
-####
-#### QUANTIFY PARAMETERS
-####
-#######################################################################################################
+max_length_reads: 30
+nh: 100
+#### QUANTIFICATION PARAMETERS ####
-# Types of miRNAs to quantify
-#mir_list: ["miRNA", "miRNA_primary_transcript", "isomirs"]
mir_list: ["miRNA", "miRNA_primary_transcript"]
-
-# Resources: miR annotations, chromosome name mappings
-# All of these are produced by the "prepare" workflow
-mirnas_anno: "results/homo_sapiens/chrY/mirna_filtered.bed"
-isomirs_anno: "results/homo_sapiens/chrY/isomirs_annotation.bed"
...
\ No newline at end of file
diff --git a/workflow/Snakefile b/workflow/Snakefile
index c8c544662ede821ac314a0e65625cd9c70ed6a45..83fb2c5afe28ad765e81c06b3979865f1daaa207 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -23,7 +23,7 @@
import os
import pandas as pd
-configfile: "../config/config.yaml"
+configfile: "config.yaml"
###############################################################################
### Global configuration
@@ -45,53 +45,29 @@ include: os.path.join("rules" , "quantify.smk")
###############################################################################
rule finish:
input:
- idx_transcriptome=expand(
- os.path.join(
+ idx_transcriptome=os.path.join(
config["output_dir"],
- "{organism}",
"transcriptome_index_segemehl.idx",
- ),
- organism=config["organism"],
),
- idx_genome=expand(
- os.path.join(
+ idx_genome=os.path.join(
config["output_dir"],
- "{organism}",
"genome_index_segemehl.idx",
- ),
- organism=config["organism"],
),
- exons=expand(
- os.path.join(
+ exons=os.path.join(
config["output_dir"],
- "{organism}",
"exons.bed",
- ),
- organism=config["organism"],
),
- header=expand(
- os.path.join(
+ header=os.path.join(
config["output_dir"],
- "{organism}",
"headerOfCollapsedFasta.sam",
- ),
- organism=config["organism"],
),
- mirnafilt=expand(
- os.path.join(
+ mirnafilt=os.path.join(
config["output_dir"],
- "{organism}",
"mirna_filtered.bed",
- ),
- organism=config["organism"],
),
- isomirs=expand(
- os.path.join(
+ isomirs=os.path.join(
config["output_dir"],
- "{organism}",
"isomirs_annotation.bed",
- ),
- organism=config["organism"],
),
maps=expand(
os.path.join(
diff --git a/workflow/rules/map.smk b/workflow/rules/map.smk
index 414f16f7564cbfdfa80f4e2777e9f9af0bfad332..659b301477b18b0cbe8bca8b2705428cc9379cc1 100644
--- a/workflow/rules/map.smk
+++ b/workflow/rules/map.smk
@@ -268,8 +268,8 @@ rule fastx_collapser:
rule mapping_genome_segemehl:
input:
reads=os.path.join(config["output_dir"], "{sample}", "collapsed.fasta"),
- genome=config["genome"],
- genome_index_segemehl=config["genome_index_segemehl"],
+ genome=os.path.join(config["output_dir"], "genome.processed.fa"),
+ genome_index_segemehl=os.path.join(config["output_dir"], "genome_index_segemehl.idx"),
output:
gmap=os.path.join(
config["output_dir"], "{sample}", "segemehlGenome_map.sam"
@@ -306,8 +306,8 @@ rule mapping_genome_segemehl:
rule mapping_transcriptome_segemehl:
input:
reads=os.path.join(config["output_dir"], "{sample}", "collapsed.fasta"),
- transcriptome=config["transcriptome"],
- transcriptome_index_segemehl=config["transcriptome_index_segemehl"],
+ transcriptome=os.path.join(config["output_dir"], "transcriptome_idtrim.fa"),
+ transcriptome_index_segemehl=os.path.join(config["output_dir"], "transcriptome_index_segemehl.idx"),
output:
tmap=os.path.join(
config["output_dir"], "{sample}", "segemehlTranscriptome_map.sam"
@@ -379,7 +379,7 @@ rule mapping_genome_oligomap:
reads=os.path.join(
config["output_dir"], "{sample}", "filtered_for_oligomap.fasta"
),
- target=config["genome"],
+ target=os.path.join(config["output_dir"], "genome.processed.fa"),
output:
gmap=os.path.join(
config["output_dir"], "{sample}", "oligoGenome_map.fa"
@@ -496,7 +496,7 @@ rule mapping_transcriptome_oligomap:
reads=os.path.join(
config["output_dir"], "{sample}", "filtered_for_oligomap.fasta"
),
- target=config["transcriptome"],
+ target=os.path.join(config["output_dir"], "transcriptome_idtrim.fa"),
output:
tmap=os.path.join(
config["output_dir"], "{sample}", "oligoTranscriptome_map.fa"
@@ -808,7 +808,7 @@ rule trans_to_gen:
"noheader_TranscriptomeMappings.sam",
),
script=os.path.join(config["scripts_dir"], "sam_trx_to_sam_gen.pl"),
- exons=config["exons"],
+ exons=os.path.join(config["output_dir"], "exons.bed"),
output:
genout=os.path.join(config["output_dir"], "{sample}", "TransToGen.sam"),
params:
@@ -861,7 +861,7 @@ rule cat_mapping:
rule add_header:
input:
- header=config["header_of_collapsed_fasta"],
+ header=os.path.join(config["output_dir"], "headerOfCollapsedFasta.sam"),
catmaps=os.path.join(
config["output_dir"], "{sample}", "catMappings.sam"
),
diff --git a/workflow/rules/prepare.smk b/workflow/rules/prepare.smk
index 2e4c1913b58171b79d95f75b01ec9c9571107a7b..2294d3f8d9631c7b754d50b4713069db950f0a06 100644
--- a/workflow/rules/prepare.smk
+++ b/workflow/rules/prepare.smk
@@ -41,53 +41,30 @@ localrules:
###############################################################################
rule finish_prepare:
input:
- idx_transcriptome=expand(
- os.path.join(
+ idx_transcriptome=os.path.join(
config["output_dir"],
- "{organism}",
"transcriptome_index_segemehl.idx",
- ),
- organism=config["organism"],
+
),
- idx_genome=expand(
- os.path.join(
+ idx_genome=os.path.join(
config["output_dir"],
- "{organism}",
"genome_index_segemehl.idx",
- ),
- organism=config["organism"],
),
- exons=expand(
- os.path.join(
+ exons=os.path.join(
config["output_dir"],
- "{organism}",
"exons.bed",
- ),
- organism=config["organism"],
),
- header=expand(
- os.path.join(
+ header=os.path.join(
config["output_dir"],
- "{organism}",
"headerOfCollapsedFasta.sam",
- ),
- organism=config["organism"],
),
- mirnafilt=expand(
- os.path.join(
+ mirnafilt=os.path.join(
config["output_dir"],
- "{organism}",
"mirna_filtered.bed",
- ),
- organism=config["organism"],
),
- isomirs=expand(
- os.path.join(
+ isomirs=os.path.join(
config["output_dir"],
- "{organism}",
"isomirs_annotation.bed",
- ),
- organism=config["organism"],
),
@@ -100,13 +77,13 @@ rule genome_process:
script=os.path.join(config["scripts_dir"], "genome_process.sh"),
output:
genome=os.path.join(
- config["output_dir"], "{organism}", "genome.processed.fa"
+ config["output_dir"], "genome.processed.fa"
),
params:
- url=lambda wildcards: config[wildcards.organism]["genome_url"],
- dir_out=os.path.join(config["output_dir"], "{organism}"),
+ url=config["genome_url"],
+ dir_out=config["output_dir"],
log:
- os.path.join(config["local_log"], "{organism}", "genome_process.log"),
+ os.path.join(config["local_log"], "genome_process.log"),
singularity:
"docker://zavolab/ubuntu:18.04"
shell:
@@ -124,14 +101,13 @@ rule filter_anno_gtf:
output:
gtf=os.path.join(
config["output_dir"],
- "{organism}",
"gene_annotations.filtered.gtf",
),
params:
- url=lambda wildcards: config[wildcards.organism]["gtf_url"],
- dir_out=os.path.join(config["output_dir"], "{organism}"),
+ url=config["gtf_url"],
+ dir_out=config["output_dir"],
log:
- os.path.join(config["local_log"], "{organism}", "filter_anno_gtf.log"),
+ os.path.join(config["local_log"], "filter_anno_gtf.log"),
singularity:
"docker://zavolab/ubuntu:18.04"
shell:
@@ -146,27 +122,25 @@ rule filter_anno_gtf:
rule extract_transcriptome_seqs:
input:
genome=os.path.join(
- config["output_dir"], "{organism}", "genome.processed.fa"
+ config["output_dir"], "genome.processed.fa"
),
gtf=os.path.join(
config["output_dir"],
- "{organism}",
"gene_annotations.filtered.gtf",
),
output:
fasta=os.path.join(
- config["output_dir"], "{organism}", "transcriptome.fa"
+ config["output_dir"], "transcriptome.fa"
),
params:
cluster_log=os.path.join(
config["cluster_log"],
- "{organism}",
"extract_transcriptome_seqs.log",
),
log:
os.path.join(
config["local_log"],
- "{organism}",
+
"extract_transcriptome_seqs.log",
),
singularity:
@@ -183,19 +157,19 @@ rule extract_transcriptome_seqs:
rule trim_fasta:
input:
fasta=os.path.join(
- config["output_dir"], "{organism}", "transcriptome.fa"
+ config["output_dir"], "transcriptome.fa"
),
script=os.path.join(config["scripts_dir"], "validation_fasta.py"),
output:
fasta=os.path.join(
- config["output_dir"], "{organism}", "transcriptome_idtrim.fa"
+ config["output_dir"], "transcriptome_idtrim.fa"
),
params:
cluster_log=os.path.join(
- config["cluster_log"], "{organism}", "trim_fasta.log"
+ config["cluster_log"], "trim_fasta.log"
),
log:
- os.path.join(config["local_log"], "{organism}", "trim_fasta.log"),
+ os.path.join(config["local_log"], "trim_fasta.log"),
singularity:
"docker://zavolab/ubuntu:18.04"
shell:
@@ -215,24 +189,21 @@ rule trim_fasta:
rule generate_segemehl_index_transcriptome:
input:
fasta=os.path.join(
- config["output_dir"], "{organism}", "transcriptome_idtrim.fa"
+ config["output_dir"], "transcriptome_idtrim.fa"
),
output:
idx=os.path.join(
config["output_dir"],
- "{organism}",
"transcriptome_index_segemehl.idx",
),
params:
cluster_log=os.path.join(
config["cluster_log"],
- "{organism}",
"generate_segemehl_index_transcriptome.log",
),
log:
os.path.join(
config["local_log"],
- "{organism}",
"generate_segemehl_index_transcriptome.log",
),
resources:
@@ -253,22 +224,20 @@ rule generate_segemehl_index_transcriptome:
rule generate_segemehl_index_genome:
input:
genome=os.path.join(
- config["output_dir"], "{organism}", "genome.processed.fa"
+ config["output_dir"], "genome.processed.fa"
),
output:
idx=os.path.join(
- config["output_dir"], "{organism}", "genome_index_segemehl.idx"
+ config["output_dir"], "genome_index_segemehl.idx"
),
params:
cluster_log=os.path.join(
config["cluster_log"],
- "{organism}",
"generate_segemehl_index_genome.log",
),
log:
os.path.join(
config["local_log"],
- "{organism}",
"generate_segemehl_index_genome.log",
),
resources:
@@ -290,18 +259,17 @@ rule get_exons_gtf:
input:
gtf=os.path.join(
config["output_dir"],
- "{organism}",
"gene_annotations.filtered.gtf",
),
script=os.path.join(config["scripts_dir"], "get_lines_w_pattern.sh"),
output:
- exons=os.path.join(config["output_dir"], "{organism}", "exons.gtf"),
+ exons=os.path.join(config["output_dir"], "exons.gtf"),
params:
cluster_log=os.path.join(
- config["cluster_log"], "{organism}", "get_exons_gtf.log"
+ config["cluster_log"], "get_exons_gtf.log"
),
log:
- os.path.join(config["local_log"], "{organism}", "get_exons_gtf.log"),
+ os.path.join(config["local_log"], "get_exons_gtf.log"),
singularity:
"docker://zavolab/ubuntu:18.04"
shell:
@@ -321,16 +289,16 @@ rule get_exons_gtf:
rule gtftobed:
input:
- exons=os.path.join(config["output_dir"], "{organism}", "exons.gtf"),
+ exons=os.path.join(config["output_dir"], "exons.gtf"),
script=os.path.join(config["scripts_dir"], "gtf_exons_bed.1.1.2.R"),
output:
- exons=os.path.join(config["output_dir"], "{organism}", "exons.bed"),
+ exons=os.path.join(config["output_dir"], "exons.bed"),
params:
cluster_log=os.path.join(
- config["cluster_log"], "{organism}", "gtftobed.log"
+ config["cluster_log"], "gtftobed.log"
),
log:
- os.path.join(config["local_log"], "{organism}", "gtftobed.log"),
+ os.path.join(config["local_log"], "gtftobed.log"),
singularity:
"docker://zavolab/r-zavolab:3.5.1"
shell:
@@ -349,19 +317,19 @@ rule gtftobed:
rule create_header_genome:
input:
genome=os.path.join(
- config["output_dir"], "{organism}", "genome.processed.fa"
+ config["output_dir"], "genome.processed.fa"
),
output:
header=os.path.join(
- config["output_dir"], "{organism}", "headerOfCollapsedFasta.sam"
+ config["output_dir"], "headerOfCollapsedFasta.sam"
),
params:
cluster_log=os.path.join(
- config["cluster_log"], "{organism}", "create_header_genome.log"
+ config["cluster_log"], "create_header_genome.log"
),
log:
os.path.join(
- config["local_log"], "{organism}", "create_header_genome.log"
+ config["local_log"], "create_header_genome.log"
),
singularity:
"docker://zavolab/samtools:1.8"
@@ -377,19 +345,19 @@ rule create_header_genome:
rule mirna_anno:
input:
genome=os.path.join(
- config["output_dir"], "{organism}", "genome.processed.fa"
+ config["output_dir"], "genome.processed.fa"
),
output:
anno=os.path.join(
- config["output_dir"], "{organism}", "raw", "mirna.gff3"
+ config["output_dir"], "mirna.gff3"
),
params:
- anno=lambda wildcards: config[wildcards.organism]["mirna_url"],
+ anno=config["mirna_url"],
cluster_log=os.path.join(
- config["cluster_log"], "{organism}", "mirna_anno.log"
+ config["cluster_log"], "mirna_anno.log"
),
log:
- os.path.join(config["local_log"], "{organism}", "mirna_anno.log"),
+ os.path.join(config["local_log"], "mirna_anno.log"),
singularity:
"docker://zavolab/ubuntu:18.04"
shell:
@@ -404,19 +372,19 @@ rule mirna_anno:
rule dict_chr:
input:
genome=os.path.join(
- config["output_dir"], "{organism}", "genome.processed.fa"
+ config["output_dir"], "genome.processed.fa"
),
output:
map_chr=os.path.join(
- config["output_dir"], "{organism}", "UCSC2ensembl.txt"
+ config["output_dir"], "UCSC2ensembl.txt"
),
params:
- map_chr=lambda wildcards: config[wildcards.organism]["map_chr_url"],
+ map_chr=config["map_chr_url"],
cluster_log=os.path.join(
- config["cluster_log"], "{organism}", "dict_chr.log"
+ config["cluster_log"], "dict_chr.log"
),
log:
- os.path.join(config["local_log"], "{organism}", "dict_chr.log"),
+ os.path.join(config["local_log"], "dict_chr.log"),
singularity:
"docker://zavolab/ubuntu:18.04"
shell:
@@ -431,24 +399,24 @@ rule dict_chr:
rule map_chr_names:
input:
anno=os.path.join(
- config["output_dir"], "{organism}", "raw", "mirna.gff3"
+ config["output_dir"], "mirna.gff3"
),
script=os.path.join(config["scripts_dir"], "map_chromosomes.pl"),
map_chr=os.path.join(
- config["output_dir"], "{organism}", "UCSC2ensembl.txt"
+ config["output_dir"], "UCSC2ensembl.txt"
),
output:
gff=os.path.join(
- config["output_dir"], "{organism}", "mirna_chr_mapped.gff3"
+ config["output_dir"], "mirna_chr_mapped.gff3"
),
params:
cluster_log=os.path.join(
- config["cluster_log"], "{organism}", "map_chr_names.log"
+ config["cluster_log"], "map_chr_names.log"
),
- column=lambda wildcards: config[wildcards.organism]["column"],
- delimiter=lambda wildcards: config[wildcards.organism]["delimiter"],
+ column=1,
+ delimiter="TAB",
log:
- os.path.join(config["local_log"], "{organism}", "map_chr_names.log"),
+ os.path.join(config["local_log"], "map_chr_names.log"),
singularity:
"docker://zavolab/perl:5.28"
shell:
@@ -469,20 +437,20 @@ rule map_chr_names:
rule filter_mir_1_anno:
input:
gff=os.path.join(
- config["output_dir"], "{organism}", "mirna_chr_mapped.gff3"
+ config["output_dir"], "mirna_chr_mapped.gff3"
),
output:
gff=os.path.join(
- config["output_dir"], "{organism}", "mirna_filtered.gff3"
+ config["output_dir"], "mirna_filtered.gff3"
),
params:
script=os.path.join(config["scripts_dir"], "filter_mir_1_anno.sh"),
cluster_log=os.path.join(
- config["cluster_log"], "{organism}", "filter_mir_1_anno.log"
+ config["cluster_log"], "filter_mir_1_anno.log"
),
log:
os.path.join(
- config["local_log"], "{organism}", "filter_mir_1_anno.log"
+ config["local_log"], "filter_mir_1_anno.log"
),
singularity:
"docker://zavolab/ubuntu:18.04"
@@ -498,19 +466,19 @@ rule filter_mir_1_anno:
rule gfftobed:
input:
gff=os.path.join(
- config["output_dir"], "{organism}", "mirna_filtered.gff3"
+ config["output_dir"], "mirna_filtered.gff3"
),
output:
bed=os.path.join(
- config["output_dir"], "{organism}", "mirna_filtered.bed"
+ config["output_dir"], "mirna_filtered.bed"
),
params:
cluster_log=os.path.join(
- config["cluster_log"], "{organism}", "gfftobed.log"
+ config["cluster_log"], "gfftobed.log"
),
- out_dir=os.path.join(config["output_dir"]),
+ out_dir=config["output_dir"]
log:
- os.path.join(config["local_log"], "{organism}", "gfftobed.log"),
+ os.path.join(config["local_log"], "gfftobed.log"),
singularity:
"docker://zavolab/bedops:2.4.35"
shell:
@@ -528,19 +496,19 @@ rule gfftobed:
rule create_index_fasta:
input:
genome=os.path.join(
- config["output_dir"], "{organism}", "genome.processed.fa"
+ config["output_dir"], "genome.processed.fa"
),
output:
genome=os.path.join(
- config["output_dir"], "{organism}", "genome.processed.fa.fai"
+ config["output_dir"], "genome.processed.fa.fai"
),
params:
cluster_log=os.path.join(
- config["cluster_log"], "{organism}", "create_index_fasta.log"
+ config["cluster_log"], "create_index_fasta.log"
),
log:
os.path.join(
- config["local_log"], "{organism}", "create_index_fasta.log"
+ config["local_log"], "create_index_fasta.log"
),
singularity:
"docker://zavolab/samtools:1.8"
@@ -556,18 +524,18 @@ rule create_index_fasta:
rule extract_chr_len:
input:
genome=os.path.join(
- config["output_dir"], "{organism}", "genome.processed.fa.fai"
+ config["output_dir"], "genome.processed.fa.fai"
),
output:
chrsize=os.path.join(
- config["output_dir"], "{organism}", "chr_size.txt"
+ config["output_dir"], "chr_size.txt"
),
params:
cluster_log=os.path.join(
- config["cluster_log"], "{organism}", "extract_chr_len.log"
+ config["cluster_log"], "extract_chr_len.log"
),
log:
- os.path.join(config["local_log"], "{organism}", "extract_chr_len.log"),
+ os.path.join(config["local_log"], "extract_chr_len.log"),
singularity:
"docker://zavolab/ubuntu:18.04"
shell:
@@ -582,20 +550,20 @@ rule extract_chr_len:
rule filter_mature_mirs:
input:
bed=os.path.join(
- config["output_dir"], "{organism}", "mirna_filtered.bed"
+ config["output_dir"], "mirna_filtered.bed"
),
output:
bed=os.path.join(
- config["output_dir"], "{organism}", "mirna_mature_filtered.bed"
+ config["output_dir"], "mirna_mature_filtered.bed"
),
params:
cluster_log=os.path.join(
- config["cluster_log"], "{organism}", "filter_mature_mirs.log"
+ config["cluster_log"], "filter_mature_mirs.log"
),
precursor="miRNA_primary_transcript",
log:
os.path.join(
- config["local_log"], "{organism}", "filter_mature_mirs.log"
+ config["local_log"], "filter_mature_mirs.log"
),
singularity:
"docker://zavolab/ubuntu:18.04"
@@ -611,21 +579,19 @@ rule filter_mature_mirs:
rule iso_anno:
input:
bed=os.path.join(
- config["output_dir"], "{organism}", "mirna_mature_filtered.bed"
+ config["output_dir"], "mirna_mature_filtered.bed"
),
chrsize=os.path.join(
- config["output_dir"], "{organism}", "chr_size.txt"
+ config["output_dir"], "chr_size.txt"
),
output:
bed=os.path.join(
config["output_dir"],
- "{organism}",
"iso_anno_5p{bp_5p}_3p{bp_3p}.bed",
),
params:
cluster_log=os.path.join(
config["cluster_log"],
- "{organism}",
"iso_anno_5p{bp_5p}_3p{bp_3p}.log",
),
bp_5p=lambda wildcards: wildcards.bp_5p,
@@ -633,7 +599,6 @@ rule iso_anno:
log:
os.path.join(
config["local_log"],
- "{organism}",
"iso_anno_5p{bp_5p}_3p{bp_3p}.log",
),
singularity:
@@ -657,19 +622,16 @@ rule iso_anno_rename:
input:
bed=os.path.join(
config["output_dir"],
- "{organism}",
"iso_anno_5p{bp_5p}_3p{bp_3p}.bed",
),
output:
bed=os.path.join(
config["output_dir"],
- "{organism}",
"iso_anno_rename_5p{bp_5p}_3p{bp_3p}.bed",
),
params:
cluster_log=os.path.join(
config["cluster_log"],
- "{organism}",
"iso_anno_rename_5p{bp_5p}_3p{bp_3p}.log",
),
bp_5p=lambda wildcards: wildcards.bp_5p,
@@ -677,7 +639,6 @@ rule iso_anno_rename:
log:
os.path.join(
config["local_log"],
- "{organism}",
"iso_anno_rename_5p{bp_5p}_3p{bp_3p}.log",
),
singularity:
@@ -700,26 +661,24 @@ rule iso_anno_concat:
bed=lambda wildcards: expand(
os.path.join(
config["output_dir"],
- "{organism}",
"iso_anno_rename_5p{bp_5p}_3p{bp_3p}.bed",
),
- organism=config["organism"],
bp_3p=config["bp_3p"],
bp_5p=config["bp_5p"],
),
output:
bed=os.path.join(
- config["output_dir"], "{organism}", "iso_anno_concat.bed"
+ config["output_dir"], "iso_anno_concat.bed"
),
params:
cluster_log=os.path.join(
- config["cluster_log"], "{organism}", "iso_anno_concat.log"
+ config["cluster_log"], "iso_anno_concat.log"
),
prefix=os.path.join(
- config["output_dir"], "{organism}", "iso_anno_rename"
+ config["output_dir"], "iso_anno_rename"
),
log:
- os.path.join(config["local_log"], "{organism}", "iso_anno_concat.log"),
+ os.path.join(config["local_log"], "iso_anno_concat.log"),
singularity:
"docker://zavolab/ubuntu:18.04"
shell:
@@ -734,19 +693,19 @@ rule iso_anno_concat:
rule iso_anno_final:
input:
bed=os.path.join(
- config["output_dir"], "{organism}", "iso_anno_concat.bed"
+ config["output_dir"], "iso_anno_concat.bed"
),
output:
bed=os.path.join(
- config["output_dir"], "{organism}", "isomirs_annotation.bed"
+ config["output_dir"], "isomirs_annotation.bed"
),
params:
cluster_log=os.path.join(
- config["cluster_log"], "{organism}", "iso_anno_final.log"
+ config["cluster_log"], "iso_anno_final.log"
),
pattern="5p0_3p0",
log:
- os.path.join(config["local_log"], "{organism}", "iso_anno_final.log"),
+ os.path.join(config["local_log"], "iso_anno_final.log"),
singularity:
"docker://zavolab/ubuntu:18.04"
shell:
diff --git a/workflow/rules/quantify.smk b/workflow/rules/quantify.smk
index 90fd57223174711bf0d854f3693c2defdf4e0364..625eea9160c5a96403b0e26fbf9a84c6adcea78f 100644
--- a/workflow/rules/quantify.smk
+++ b/workflow/rules/quantify.smk
@@ -74,7 +74,7 @@ rule finish_quantify:
rule bamtobed:
input:
alignment=os.path.join(
- config["quantify_input_dir"],
+ config["output_dir"],
"{sample}",
"convertedSortedMappings_{sample}.bam",
),
@@ -143,7 +143,9 @@ rule intersect_mirna:
alignment=os.path.join(
config["output_dir"], "{sample}", "sorted.alignments.bed12"
),
- mirna=config["mirnas_anno"],
+ mirna=os.path.join(
+ config["output_dir"], "mirna_filtered.bed"
+ ),
output:
intersect=os.path.join(
config["output_dir"], "{sample}", "intersect_mirna.bed"
@@ -178,7 +180,9 @@ rule intersect_mirna:
# alignment=os.path.join(
# config["output_dir"], "{sample}", "sorted.alignments.bed12"
# ),
-# isomirs=config["isomirs_anno"],
+# isomirs=os.path.join(
+# config["output_dir"], "isomirs_annotation.bed",
+# ),
# output:
# intersect=os.path.join(
# config["output_dir"], "{sample}", "intersect_isomirs.bed"