Merged in release-polish (pull request #149)

Release polish

Approved-by: Brian Sanderson

bin/help/amplicon.nf

@@ -2,6 +2,8 @@ def help(){
   println '''
 Parameter | Default | Description
 
+WORKFLOW NOT OFFICALLY SUPPORTED AT THIS TIME. 
+
 '''
 }
 

bin/help/atac.nf

@@ -12,10 +12,13 @@ Parameter | Default | Description
 --pattern | '*_R{1,2}*' | The expected R1 / R2 matching pattern. The default value will match reads with names like this READ_NAME_R1_MoreText.fastq.gz or READ_NAME_R1.fastq.gz
 --read_type | PE | Options: PE and SE. Default: PE. Type of reads: paired end (PE) or single end (SE).
 --concat_lanes | false | Options: false and true. Default: false. If this boolean is specified, FASTQ files will be concatenated by sample. This option is used in cases where samples are divided across individual sequencing lanes.
+--csv_input | null | Provide a CSV manifest file with the header: "sampleID,lane,fastq_1,fastq_2". See the repository wiki for an example file. Fastq_2 is optional and used only in PE data. Fastq files can either be absolute paths to local files, or URLs to remote files. If remote URLs are provided, `--download_data` must be specified.
+--download_data | null | Requires `--csv_input`. When specified, read data in the CSV manifest will be downloaded from provided URLs. 
 
---gen_org | mouse | Options: mouse and human.
+--gen_org | mouse | Options: mouse or human.
+--genome_build | 'GRCm38' | Options: GRCm38 or GRCm39
 
---effective_genome_size | The length of the “mappable” genome. | Mouse only - Please see : 'https://deeptools.readthedocs.io/en/develop/content/feature/effectiveGenomeSize.html'.
+--effective_genome_size | The length of the “mappable” genome. | See : 'https://deeptools.readthedocs.io/en/develop/content/feature/effectiveGenomeSize.html'.
                         
 --chain | null | The default value for Mouse Reference Strain -  g2gtools chain file to adjust coordinates to reference                                                              
 

bin/help/chipseq.nf

@@ -13,7 +13,8 @@ Parameter | Default | Description
 --read_type | PE | Options: PE and SE. Default: PE. Type of reads: paired end (PE) or single end (SE).
 
 --gen_org | mouse | Options: mouse and human.
-                        
+--genome_build | 'GRCm38' | Mouse specific. Options: GRCm38 or GRCm39. If gen_org == human, build defaults to GRCm38.
+
 --fragment_size | 200 |  Number of base pairs to extend single-end reads when creating bigWig files (Default: 200)
 --fingerprint_bins | 500000 | Number of genomic bins to use when generating the deepTools fingerprint plot. Larger numbers will give a smoother profile, but take longer to run (Default: 500000)                              
 --gtf      | The full path to GTF file for annotating peaks and the GTF file should resemble the Ensembl format
@@ -28,8 +29,6 @@ Parameter | Default | Description
 --macs_gsize | Effective genome size parameter required by MACS2 | if this parameter is not specified then the MACS2 peak-calling and differential analysis will be skipped                            
 --blacklist | The BED format file, if provided, alignments that overlap with the regions in this file will be filtered out | Please see : 'https://sites.google.com/site/anshulkundaje/projects/blacklists'
 
---non_directional | true | Options: true and false. Selecting this option for non-directional RRBS libraries will screen quality-trimmed sequences for CAA or CGA at the start of the read and, if found, removes the first two base pairs.
-
 --trimLength | 30 | Discard reads that became shorter than length 'INT' because of either quality or adapter trimming. A value of 0 effectively disables this behaviour.
 --qualThreshold | 30 | Trim low-quality ends from reads in addition to adapter removal. For RRBS samples, quality trimming will be performed first, and adapter trimming is carried in a second round. Other files are quality and adapter trimmed in a single pass. The algorithm is the same as the one used by BWA (Subtract INT from all qualities; compute partial sums from all indices to the end of the sequence; cut sequence at the index at which the sum is minimal).
 --adapOverlap | 1 | Stringency for overlap with adapter sequence required to trim a sequence. Defaults to a very stringent setting of 1, i.e. even a single base pair of overlapping sequence will be trimmed of the 3' end of any read.

bin/help/pdx_wes.nf

@@ -15,46 +15,29 @@ Parameter | Default | Description
 --csv_input | null | Provide a CSV manifest file with the header: "sampleID,lane,fastq_1,fastq_2". See the repository wiki for an example file. Fastq_2 is optional and used only in PE data. Fastq files can either be absolute paths to local files, or URLs to remote files. If remote URLs are provided, `--download_data` must be specified.
 --download_data | null | Requires `--csv_input`. When specified, read data in the CSV manifest will be downloaded from provided URLs. 
 
---gen_org | mouse | Options: mouse and human.
+--gen_org | human | Options: human only.
 
---ref_fa | Mouse: '/projects/omics_share/mouse/GRCm38/genome/sequence/ensembl/v102/Mus_musculus.GRCm38.dna.toplevel.fa' 
-         | Human: '/projects/omics_share/human/GRCh38/genome/sequence/gatk/Homo_sapiens_assembly38.fasta'
-         | The reference fasta to be used throughout the process for alignment as well as any downstream analysis, points to human reference when --gen_org human. JAX users should not change this parameter.
+--ref_fa | '/projects/omics_share/human/GRCh38/genome/sequence/gatk/Homo_sapiens_assembly38.fasta' | The reference fasta to be used throughout the process for alignment as well as any downstream analysis. JAX users should not change this parameter.
 
---ref_fa_indices | Mouse: '/projects/omics_share/mouse/GRCm38/genome/indices/ensembl/v102/bwa/Mus_musculus.GRCm38.dna.toplevel.fa' 
-                 | Human: '/projects/omics_share/human/GRCh38/genome/indices/gatk/bwa/Homo_sapiens_assembly38.fasta'
-                 | Pre-compiled BWA index files, points to human reference when --gen_org human. JAX users should not change this parameter.
+--ref_fa_indices | '/projects/omics_share/human/GRCh38/genome/indices/gatk/bwa/Homo_sapiens_assembly38.fasta' | Pre-compiled BWA index files. JAX users should not change this parameter.
 
 --min_pct_hq_reads | 0.0 | The minimum percent of high-quality reads passing when trimming the fastq files.
 
---target_gatk | Mouse: '/projects/omics_share/mouse/GRCm38/supporting_files/capture_kit_files/agilent/v2/S32371113_mouse_exon_V2.bare.bed' 
-              | Human: '/projects/omics_share/human/GRCh38/supporting_files/capture_kit_files/agilent/v7/S31285117_MergedProbes_no_gene_names.bed'
-              | A bed file with WES target intervals as defined in the capture array used in the data, points to human bed file when --gen_org human. NOTE: This file MUST reflect the capture array used to generate your data.
+--target_gatk | '/projects/omics_share/human/GRCh38/supporting_files/capture_kit_files/agilent/v7/S31285117_MergedProbes_no_gene_names.bed' | A bed file with WES target intervals as defined in the capture array used in the data. NOTE: This file MUST reflect the capture array used to generate your data.
 
---target_picard | Mouse: '/projects/omics_share/mouse/GRCm38/supporting_files/capture_kit_files/agilent/v2/S32371113_mouse_exon_V2.bare.picard.interval_list' 
-                | Human: '/projects/omics_share/human/GRCh38/supporting_files/capture_kit_files/agilent/v7/S31285117_MergedProbes_no_gene_names.picard.interval_list'
-                | A GATK interval file covering WES target intervals. Used in calculating coverage metrics. NOTE: This file MUST reflect the capture array used to generate your data.
+--target_picard | '/projects/omics_share/human/GRCh38/supporting_files/capture_kit_files/agilent/v7/S31285117_MergedProbes_no_gene_names.picard.interval_list' | A GATK interval file covering WES target intervals. Used in calculating coverage metrics. NOTE: This file MUST reflect the capture array used to generate your data.
 
---bait_picard | Mouse: '/projects/omics_share/mouse/GRCm38/supporting_files/capture_kit_files/agilent/v2/S32371113_mouse_exon_V2.bare.picard.interval_list' 
-              | Human: '/projects/omics_share/human/GRCh38/supporting_files/capture_kit_files/agilent/v7/S31285117_MergedProbes_no_gene_names.picard.interval_list'
-              | A GATK interval file covering WES target intervals. Used in calculating coverage metrics. This file can be the same as the interval file,  NOTE: This file MUST reflect the capture array used to generate your data.
+--bait_picard | '/projects/omics_share/human/GRCh38/supporting_files/capture_kit_files/agilent/v7/S31285117_MergedProbes_no_gene_names.picard.interval_list' | A GATK interval file covering WES target intervals. Used in calculating coverage metrics. This file can be the same as the interval file,  NOTE: This file MUST reflect the capture array used to generate your data.
 
 --mismatch_penalty | -B 8 | The BWA penalty for a mismatch.
 --call_val | 50 | The minimum phred-scaled confidence threshold at which variants should be called.
 --ploidy_val | '-ploidy 2' | Sample ploidy
 
---dbSNP | Mouse: '/projects/omics_share/mouse/GRCm38/genome/annotation/snps_indels/GCA_000001635.6_current_ids.vcf.gz' 
-        | Human: '/projects/omics_share/human/GRCh38/genome/annotation/snps_indels/dbsnp_151.vcf.gz'
-        | The dbSNP database contains known single nucleotide polymorphisms, and is used in the annotation of known variants. Points to human dbSNP when --gen_org human. JAX users should not change this parameter.
+--dbSNP | '/projects/omics_share/human/GRCh38/genome/annotation/snps_indels/dbsnp_151.vcf.gz' | The dbSNP database contains known single nucleotide polymorphisms, and is used in the annotation of known variants. Points to human dbSNP when --gen_org human. JAX users should not change this parameter.
 
---gen_ver | Mouse: 'GRCm38.99' 
-          | Human: 'hg38'
-          | snpEff genome version. Sets to 'hg38' when --gen_org human JAX users should not change this parameter.
-
---snpEff_config | Mouse: '/projects/omics_share/mouse/GRCm38/genome/indices/snpEff_5_1/snpEff.config' 
-                | Human: '/projects/omics_share/human/GRCh38/genome/indices/snpEff_5_1/snpEff.config'
-                | The configuration file used while running snpEff, points to human snpEff file when --gen_org human. JAX users should not change this parameter.
+--gen_ver | 'hg38' | snpEff genome version. Sets to 'hg38' when --gen_org human JAX users should not change this parameter.
 
+--snpEff_config | Human: '/projects/omics_share/human/GRCh38/genome/indices/snpEff_5_1/snpEff.config' | The configuration file used while running snpEff, points to human snpEff file when --gen_org human. JAX users should not change this parameter.
 
 --gold_std_indels | '/projects/omics_share/human/GRCh38/genome/annotation/snps_indels/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz’ | Human Only - Used in GATK BaseRecalibrator. JAX users should not change this parameter.
 --phase1_1000G | '/projects/omics_share/human/GRCh38/genome/annotation/snps_indels/1000G_phase1.snps.high_confidence.hg38.vcf.gz' | Human Only - Used in GATK BaseRecalibrator. JAX users should not change this parameter.

bin/help/rnaseq.nf

@@ -16,13 +16,21 @@ Parameter | Default | Description
 --download_data | null | Requires `--csv_input`. When specified, read data in the CSV manifest will be downloaded from provided URLs. 
 
 --gen_org | mouse | Options: mouse and human.
+--genome_build | 'GRCm38' | Mouse specific. Options: GRCm38 or GRCm39. If gen_org == human, build defaults to GRCm38.
 
 --pdx | false | Options: true or false. If 'true' Xenome is run to remove mouse reads from samples. 
 --xenome_prefix | '/projects/compsci/omics_share/human/GRCh38/supporting_files/xenome/trans_human_GRCh38_84_NOD_based_on_mm10_k25' | Pre-compiled Xenome classification index files. Used if PDX analysis is specified. 
 
 --min_pct_hq_reads | 0.0 | The minimum percent of high-quality reads passing when trimming the fastq files to continue with the analysis. 0.0 disables this filter.
 --hq_pct | 70 | The percentage of bases within a read that must be high quality for the read to pass filtering"
 
+--strandedness_ref | Mouse: '/projects/compsci/omics_share/human/GRCh38/transcriptome/indices/ensembl/v104/kallisto/kallisto_index'
+                   | Human: '/projects/compsci/omics_share/human/GRCh38/transcriptome/indices/ensembl/v104/kallisto/kallisto_index' 
+                   | Modfied kallisto index file used in strandedness determination. 
+--strandedness_gtf | Mouse: '/projects/compsci/omics_share/mouse/GRCm38/transcriptome/annotation/ensembl/v102/Mus_musculus.GRCm38.102.gtf'
+                   | Human: '/projects/compsci/omics_share/human/GRCh38/transcriptome/annotation/ensembl/v104/Homo_sapiens.GRCh38.104.gtf' 
+                   | GTF file used with kallisto index file used in strandedness determination. 
+
 --rsem_ref_files | /projects/omics_share/mouse/GRCm38/transcriptome/indices/ensembl/v102/bowtie2 | Pre-compiled index files. Refers to human indices when --gen_org human. JAX users should not change this, unless using STAR indices.
 --rsem_ref_prefix | 'Mus_musculus.GRCm38.dna.toplevel' | Prefix for index files. JAX users should not change this, unless using STAR indices. Refers to human indices when --gen_org human.
 --seed_length | 25 | 'Seed length used by the read aligner. Providing the correct value is important for RSEM. If RSEM runs Bowtie, it uses this value for Bowtie's seed length parameter.'

bin/help/rrbs.nf

@@ -12,10 +12,13 @@ Parameter | Default | Description
 --pattern | '*_R{1,2}*' | The expected R1 / R2 matching pattern. The default value will match reads with names like this READ_NAME_R1_MoreText.fastq.gz or READ_NAME_R1.fastq.gz
 --read_type | PE | Options: PE and SE. Default: PE. Type of reads: paired end (PE) or single end (SE).
 --concat_lanes | false | Options: false and true. Default: false. If this boolean is specified, FASTQ files will be concatenated by sample. This option is used in cases where samples are divided across individual sequencing lanes.
+--csv_input | null | Provide a CSV manifest file with the header: "sampleID,lane,fastq_1,fastq_2". See the repository wiki for an example file. Fastq_2 is optional and used only in PE data. Fastq files can either be absolute paths to local files, or URLs to remote files. If remote URLs are provided, `--download_data` must be specified.
+--download_data | null | Requires `--csv_input`. When specified, read data in the CSV manifest will be downloaded from provided URLs. 
 
 --gen_org | mouse | Options: mouse and human.
+--genome_build | 'GRCm38' | Mouse specific. Options: GRCm38 or GRCm39. If gen_org == human, build defaults to GRCm38.
 
---non_direction | true | Options: true and false. Selecting this option for non-directional RRBS libraries will screen quality-trimmed sequences for CAA or CGA at the start of the read and, if found, removes the first two base pairs. 
+--non_directional | true | Options: true and false. Selecting this option for non-directional RRBS libraries will screen quality-trimmed sequences for CAA or CGA at the start of the read and, if found, removes the first two base pairs. 
 
 --trimLength | 30 | Discard reads that became shorter than length 'INT' because of either quality or adapter trimming. A value of 0 effectively disables this behaviour.
 --qualThreshold | 30 | Trim low-quality ends from reads in addition to adapter removal. For RRBS samples, quality trimming will be performed first, and adapter trimming is carried in a second round. Other files are quality and adapter trimmed in a single pass. The algorithm is the same as the one used by BWA (Subtract INT from all qualities; compute partial sums from all indices to the end of the sequence; cut sequence at the index at which the sum is minimal).

bin/help/wes.nf

@@ -12,9 +12,13 @@ Parameter | Default | Description
 --pattern | '*_R{1,2}*' | The expected R1 / R2 matching pattern. The default value will match reads with names like this READ_NAME_R1_MoreText.fastq.gz or READ_NAME_R1.fastq.gz
 --read_type | PE | Options: PE and SE. Default: PE. Type of reads: paired end (PE) or single end (SE).
 --concat_lanes | false | Options: false and true. Default: false. If this boolean is specified, FASTQ files will be concatenated by sample. This option is used in cases where samples are divided across individual sequencing lanes.
+--csv_input | null | Provide a CSV manifest file with the header: "sampleID,lane,fastq_1,fastq_2". See the repository wiki for an example file. Fastq_2 is optional and used only in PE data. Fastq files can either be absolute paths to local files, or URLs to remote files. If remote URLs are provided, `--download_data` must be specified.
+--download_data | null | Requires `--csv_input`. When specified, read data in the CSV manifest will be downloaded from provided URLs. 
+
 --run_gvcf | false | Options: false and true. Default: false. If this boolean is specified, GCVF output will be generated.
 
 --gen_org | mouse | Options: mouse and human.
+--genome_build | 'GRCm38' | Mouse specific. Options: GRCm38 or GRCm39. If gen_org == human, build defaults to GRCm38.
 
 --ref_fa | Mouse: '/projects/omics_share/mouse/GRCm38/genome/sequence/ensembl/v102/Mus_musculus.GRCm38.dna.toplevel.fa' 
          | Human: '/projects/omics_share/human/GRCh38/genome/sequence/gatk/Homo_sapiens_assembly38.fasta'

bin/help/wgs.nf

@@ -12,9 +12,13 @@ Parameter | Default | Description
 --pattern | '*_R{1,2}*' | The expected R1 / R2 matching pattern. The default value will match reads with names like this READ_NAME_R1_MoreText.fastq.gz or READ_NAME_R1.fastq.gz
 --read_type | PE | Options: PE and SE. Default: PE. Type of reads: paired end (PE) or single end (SE).
 --concat_lanes | false | Options: false and true. Default: false. If this boolean is specified, FASTQ files will be concatenated by sample. This option is used in cases where samples are divided across individual sequencing lanes.
+--csv_input | null | Provide a CSV manifest file with the header: "sampleID,lane,fastq_1,fastq_2". See the repository wiki for an example file. Fastq_2 is optional and used only in PE data. Fastq files can either be absolute paths to local files, or URLs to remote files. If remote URLs are provided, `--download_data` must be specified.
+--download_data | null | Requires `--csv_input`. When specified, read data in the CSV manifest will be downloaded from provided URLs. 
+
 --run_gvcf | false | Options: false and true. Default: false. If this boolean is specified, GCVF output will be generated.
 
 --gen_org | mouse | Options: mouse and human.
+--genome_build | 'GRCm38' | Mouse specific. Options: GRCm38 or GRCm39. If gen_org == human, build defaults to GRCm38.
 
 --ref_fa | Mouse: '/projects/omics_share/mouse/GRCm38/genome/sequence/ensembl/v102/Mus_musculus.GRCm38.dna.toplevel.fa' 
          | Human: '/projects/omics_share/human/GRCh38/genome/sequence/gatk/Homo_sapiens_assembly38.fasta'