From e8ba2ed962e91fba8a611cf7e500966c259291a8 Mon Sep 17 00:00:00 2001
From: IvisTang <me@ivistang.com>
Date: Wed, 17 Dec 2025 23:27:49 +0800
Subject: [PATCH] =?UTF-8?q?=E6=9B=B4=E6=96=B0=20.gitignore=EF=BC=8C?=
 =?UTF-8?q?=E6=B7=BB=E5=8A=A0=20run.status.json=EF=BC=9B=E5=88=A0=E9=99=A4?=
 =?UTF-8?q?=E6=97=A7=E7=9A=84=20mapping.sh=20=E8=84=9A=E6=9C=AC=E5=B9=B6?=
 =?UTF-8?q?=E6=B7=BB=E5=8A=A0=E6=96=B0=E7=9A=84=2001.mapping.sh=20?=
 =?UTF-8?q?=E8=84=9A=E6=9C=AC?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .gitignore                                |  3 ++-
 99.scripts/workflow/plastid/01.mapping.sh | 18 ++++++++++++++++++
 99.scripts/workflow/plastid/mapping.sh    | 15 ---------------
 3 files changed, 20 insertions(+), 16 deletions(-)
 create mode 100755 99.scripts/workflow/plastid/01.mapping.sh
 delete mode 100644 99.scripts/workflow/plastid/mapping.sh

diff --git a/.gitignore b/.gitignore
index 8215a70..4c68590 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,9 +10,10 @@
 05.reduce_redundancy/*
 05.orthology_inference/*
 06.phylogeny_reconstruction/*
+10.plastid/*
 98.results/*
 99.scripts/bucky/
 99.scripts/phyparts/
-run.status
+run.status.json
 !*/_description.md
 tmp/
diff --git a/99.scripts/workflow/plastid/01.mapping.sh b/99.scripts/workflow/plastid/01.mapping.sh
new file mode 100755
index 0000000..1d394c7
--- /dev/null
+++ b/99.scripts/workflow/plastid/01.mapping.sh
@@ -0,0 +1,18 @@
+#! /bin/bash
+set -e
+THREADS=${THREADS:-6}
+if [ "$#" -ne 4 ]; then
+    echo "Usage: $0 <reference_genome> <fastq_1> <fastq_2> <output_prefix>"
+    exit 1
+fi
+
+ref=$1
+fq1=$2
+fq2=$3
+out=$4
+outdir=$(dirname "$out")
+mkdir -p "$outdir"
+hisat2 -p "$THREADS" --dta -x "$ref" -1 "$fq1" -2 "$fq2" -S "${out}.sam"
+samtools view -b -@ "$THREADS" "${out}.sam" | samtools sort -@ "$THREADS" -o "${out}.sorted.bam" --write-index
+rm "${out}.sam"
+echo "Mapping completed. Sorted BAM file is at ${out}.sorted.bam"
diff --git a/99.scripts/workflow/plastid/mapping.sh b/99.scripts/workflow/plastid/mapping.sh
deleted file mode 100644
index 2f01d25..0000000
--- a/99.scripts/workflow/plastid/mapping.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-#! /usr/bash
-if [ "$#" -ne 5 ]; then
-    echo "Usage: $0 <reference_genome> <fastq_1> <fastq_2> <output_directory> <stem>"
-    exit 1
-fi
-ref=$1
-fq1=$2
-fq2=$3
-outdir=$4
-stem=$5
-mkdir -p "$outdir"
-hisat -p 4 --dta -x "$ref" -1 "$fq1" -2 "$fq2" -S "${outdir}/${stem}.sam"
-samtools view -b -@ 4 "${outdir}/${stem}.sam" | samtools sort -@ 4 -o "${outdir}/${stem}.sorted.bam" --write-index
-rm "${outdir}/${stem}.sam"
-echo "Mapping completed. Sorted BAM file is at ${outdir}/${stem}.sorted.bam"