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Cristianetaniguti · Nov 23, 2022 · 20f289a · 20f289a
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diff --git a/pipelines/EmpiricalMaps/EmpiricalMaps.changelog.md b/pipelines/EmpiricalMaps/EmpiricalMaps.changelog.md
@@ -13,3 +13,9 @@ It also has the options to:
 
 * Include or not multiallelic (MNP) markers
 * Apply filters using VCFtools
+
+This workflow uses:
+
+* Diploid bi-parental F1 population
+* Genomic positions for markers order
+* A single chromosome from a reference genome
diff --git a/pipelines/EmpiricalSNPCalling/EmpiricalSNPCalling.changelog.md b/pipelines/EmpiricalSNPCalling/EmpiricalSNPCalling.changelog.md
@@ -9,4 +9,10 @@ The workflow also include de options to:
 * Remove of not the read duplicates 
 * Perform the Hard Filtering in GATK results
 * Replace the VCF AD format field by counts from BAM files
-* Run MCHap software to build haplotypes based on GATK called markers
+* Run MCHap software to build haplotypes based on GATK called markers
+
+This workflow requires:
+
+* Diploid or polyploid specie
+* Single-end reads
+* A reference genome
diff --git a/pipelines/PreprocessingReads/PreprocessingReads.changelog.md b/pipelines/PreprocessingReads/PreprocessingReads.changelog.md
@@ -1,9 +1,9 @@
-# 1.0.1
+# 1.0.0
 
-- Automatic releases
+Initial release
 
-- Testing changelog
+This workflow use STACKS process_radtags plugin to demultiplex GBS FASTQ files, filter by presence of the enzyme cut site and sequence quality. The cutadapt software is also implemented to remove adaptors sequences.
 
-# 1.0.0
+This workflow requires:
 
-Initial release
+* Genotyping-by-sequencing data
diff --git a/pipelines/SimulatedReads/SimulatedReads.changelog.md b/pipelines/SimulatedReads/SimulatedReads.changelog.md
@@ -1,3 +1,23 @@
 # 1.0.0
 
 Initial release
+
+This workflow perform simulations of one or more (defined by `number_of_families`) bi-parental outcrossing population haplotypes using PedigreeSim software based on a provided linkage map and SNP markers. It uses RADinitio software, the simulated haplotypes and a reference genome to also simulate genotyping-by-sequencing read sequences. After, it performs the SNP and genotype calling and builds 68 linkage maps from the combinations:
+
+* SNP calling: GATK and Freebayes
+* Dosage/genotype calling: updog, polyRAD and SuperMASSA
+* Linkage map build software: OneMap 3.0 and GUSMap
+* Using genotype probabilities from GATK, Freebayes, updog, polyRAD and SuperMASSA, and a global error rate of 5% and 0.001% in the OneMap HMM.
+
+It also has the options to:
+
+* Include or not multiallelic (MNP) markers
+* Apply filters using VCFtools
+
+This workflow uses:
+
+* A reference linkage map
+* A reference VCF file 
+* A single chromosome from a reference genome
+* Diploid bi-parental F1 population
+* Genomic positions for markers order