Update README.md

Author: mobinasri

README.md

@@ -88,6 +88,7 @@ Here is a list of input parameters for hmm_flagger_end_to_end_with_mapping.wdl (
 |hap2AssemblyFasta| Path to uncompressed or gzip-compressed fasta file of the 2nd haplotype.| File | **No Default (Mandatory)** |
 |readFiles| An array of read files. Their format can be either fastq, fq, fastq.gz, fq.gz, bam or cram. For cram format referenceFastaForReadExtraction should also be passed.| Array[File] | **No Default (Mandatory)** |
 |presetForMapping| Paremeter preset should be selected based on aligner and sequencing platform. Common presets are map-pb/map-hifi/map-ont for minimap2, map-pb/map-ont for winnowmap and hifi-haploid/hifi-haploid-complete/hifi-diploid/ont-haploid-complete for veritymap| String | **No Default (Mandatory)** |
+|alphaTsv| The dependency factors for adjusting emission parameters with previous emission. This parameter is a tsv file with 4 rows and 4 columns with no header line. All numbers should be between 0 and 1. | File |**No Default (Mandatory)**  |
 |aligner| Name of the aligner. It can be either minimap2, winnowmap or veritymap.| String | winnowmap |
 |kmerSize| The kmer size for using minimap2 or winnowmap. With winnowmap kmer size should be 15 and with minimap2 kmer size should be 17 and 19 for using the presets map-ont and map-hifi/map-pb respectively.| Int | 15 |
 |alignerOptions| Aligner options. It can be something like '--eqx --cs -Y -L -y' for minimap2/winnowmap. Note that if assembly is diploid and aligner is either minimap2 or winnowmap '-I8g' is necessary. If the reads contain modification tags and these tags are supposed to be present in the final alignment file, alignerOptions should contain '-y' and the aligner should be either minimap2 or winnowmap. If running secphase is enabled it is recommended to add '-p0.5' to alignerOptions; it will keep more secondary alignments so secphase will have more candidates per read. For veritymap '--careful' can be used but not recommended for whole-genome assembly since it increases the runtime dramatically.| String | --eqx -Y -L -y |
@@ -128,10 +129,9 @@ Here is a list of input parameters for hmm_flagger_end_to_end_with_mapping.wdl (
 |convergenceToleranceForFlagger| Convergence tolerance. The EM iteration will stop once the difference between all model parameter values in two consecutive iterations is less than this value. | Flaot| 0.001|
 |maxHighMapqRatio | Maximum ratio of high mapq coverage for duplicated component | Float | 0.25 |
 |flaggerMoreOptions | More options for HMM-Flagger provided in a single string | String | No Default (Optional) |
-|alphaTsv| The dependency factors for adjusting emission parameters with previous emission. This parameter is a tsv file with 4 rows and 4 columns with no header line. All numbers should be between 0 and 1. | File | all alpha factors set to 0 |
 |modelType | Model type can be either 'gaussian', 'negative_binomial', or 'trunc_exp_gaussian' | String | 'trunc_exp_gaussian'|
 |flaggerMinimumBlockLenArray | Array of minimum lengths for converting short non-Hap blocks into Hap blocks. Given numbers should be related to the states Err, Dup and Col respectively. | Array[Int] | [0,0,0]|      |flaggerMemSize | Memory size in GB for running HMM-Flagger | Int | 32 |
-|flaggerThreadCount | Number of threads for running HMM-Flagger | Int | 8 |
+|flaggerThreadCount | Number of threads for running HMM-Flagger | Int | 16 |
 |flaggerDockerImage | Docker image for HMM-Flagger | String | mobinasri/flagger:v1.0.0 | 
 |enableOutputtingBigWig| If true it will make bigwig files from cov files and output them. bigwig files can be easily imported into IGV sessions | Boolean | true |
 |enableOutputtingBam| If true it will make bigwig files from cov files and output them. bigwig files can be easily imported into IGV sessions | Boolean | false |