Merge develop for v0.2.0 and update changelog

.circ

@@ -0,0 +1,42 @@
+# add project folder to PATH
+projectDir=$(dirname $(realpath $_))
+export PATH=${projectDir}:$PATH
+
+NXF_OPTIONS=$(nextflow help run | egrep -o '\-\w+\.?' | sort -u)
+PIPE_OPTIONS=$(egrep log chipseq-pipeline.nf | egrep -o '\-{2}[^ ]+ ')
+
+_ci() {
+    local cur prev
+
+    cur=${COMP_WORDS[COMP_CWORD]}
+    prev=${COMP_WORDS[COMP_CWORD-1]}
+
+    case ${COMP_CWORD} in
+        1)
+            COMPREPLY=($(compgen -W "run validate cleanup" ${cur}))
+            ;;
+        [2-9]|[1-9][0-9])
+            case ${COMP_WORDS[1]} in
+                run)
+                    case "${cur}" in
+                        -*)
+                            COMPREPLY=($(compgen -o default -W "$NXF_OPTIONS $PIPE_OPTIONS" -- ${cur}))
+                            ;;
+                        *)
+                            COMPREPLY=($(compgen -o default))
+                            ;;
+                    esac
+                    ;;
+                validate)
+                    COMPREPLY=($(compgen -f ${cur}))
+                    ;;
+            esac
+            ;;
+        *)
+            COMPREPLY=()
+            ;;
+    esac
+}
+
+# add command autocompletion
+complete -o nospace -F _ci ci

CHANGELOG.md

@@ -1,5 +1,14 @@
 # ChIP-nf Changelog
 
+## Version 0.2.0
+
+- Update groupTuple for merging and fix input sorting for Zerone - resolves #3
+- Add paramter to set MACS2 temp dir and set default to process folder
+- Use global fragment length from cli option when not shifting - close #2
+- Fix issue with samples using the same control
+- Add more test data
+- Update pipeline with Zerone process and change config and readme
+
 ## Version 0.1.0
 
 First version

README.adoc

@@ -4,7 +4,7 @@
 :macs2-outfiles: https://github.com/taoliu/MACS#output-files
 :pvalue: pass:q[[red]#___-log_10(P)___#]
 :circle-shield: https://circleci.com/gh/guigolab/chip-nf.svg?style=shield
-:nf-shield: https://img.shields.io/badge/nextflow-%E2%89%A50.17.0-blue.svg
+:nf-shield: https://img.shields.io/badge/nextflow-%E2%89%A50.23.1-blue.svg
 
 image:{nf-shield}["Nextflow", link="https://nextflow.io", window="_blank"]
 image:{circle-shield}["CircleCI status", link="https://circleci.com/gh/guigolab/chip-nf", window="_blank"]