fix: fix paths in scripts

MoTrPAC · Mar 8, 2023 · 5940239 · 5940239
1 parent 19ab3ef
commit 5940239
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/src/atac-post-process-human-wrapper.sh b/src/atac-post-process-human-wrapper.sh
@@ -46,9 +46,9 @@ bash src/align_stats.sh $NUM_CORES "$MOUNT_DIR"/$LOCAL_ATAC_OUT_DIR "$MOUNT_DIR"
 
 # Create final qc report merging the metadata and workflow qc scores
 echo "Generating merged qc reports..."
-Rscript src/merge_atac_qc_human.R -w "$MOUNT_DIR"/$LOCAL_ATAC_OUT_DIR/$SAMPLE_METADATA_FILENAME -q "$MOUNT_DIR"/$LOCAL_ATAC_OUT_DIR/qc/"$BATCH_PREFIX"_qc.tsv -a "$MOUNT_DIR"/$LOCAL_ATAC_OUT_DIR/merged_chr_info.csv -o "$MOUNT_DIR"/${ATAC_OUTPUT_DIR#"gs://"}/
+Rscript src/merge_atac_qc_human.R -w "$MOUNT_DIR/$LOCAL_ATAC_OUT_DIR/$SAMPLE_METADATA_FILENAME" -q "$MOUNT_DIR"/$LOCAL_ATAC_OUT_DIR/croo/final/qc/"$BATCH_PREFIX"_qc.tsv -a "$MOUNT_DIR"/$LOCAL_ATAC_OUT_DIR/merged_chr_info.csv -o "$MOUNT_DIR"/${ATAC_OUTPUT_DIR#"gs://"}/
 
 echo "Generating sample counts matrix..."
-bash src/encode_to_count_matrix_human.sh $ATAC_OUTPUT_DIR "$(pwd)"/src/ $NUM_CORES
+bash src/encode_to_count_matrix_human.sh "$MOUNT_DIR/$LOCAL_ATAC_OUT_DIR" "$(pwd)"/src/ $NUM_CORES
 
 echo "Done!"
diff --git a/src/qc2tsv.sh b/src/qc2tsv.sh
@@ -14,7 +14,7 @@ cd "$random_string" || exit
 gsutil ls "$gcp_path"/*/*/qc/qc.json >file_list.txt
 echo "Done creating file list"
 qc2tsv --file file_list.txt --collapse-header >"$outfile_name"
-gsutil mv "$outfile_name" "$gcp_path"/final/
+gsutil mv "$outfile_name" "$gcp_path"
 echo "Done creating atac-seq qc report"
 
 cd ..