Samtools index automatic copy/link is not functional with cross-device links

[hexylena]

$ cat call-renameIndex-2-...-0/command   

bash -c '
# Make sure outputBamPath does not exist.
if [ ! -f ./ILX/ILX.bam.bai ]
then
    mkdir -p "$(dirname ./ILX/ILX.bam.bai)"
    ln /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/ILX.bam ./ILX/ILX.bam.bai || cp /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/ILX.bam ./ILX/ILX.bam.bai
fi
samtools index \
--threads 0 \
./ILX/ILX.bam.bai ./ILX/ILX.bam.bai
'

I manually took the set -e out, thinking that would fix it (it should, ne?) but the job still errors. Clearly this was done intentionally to solve exactly the issue I face but, there's something not working or somewhere a

$ cat call-renameIndex-2-...-0/stderr.txt 
ln: ./ILX/ILX.bam.bai: Invalid cross-device link
samtools index: use -M to enable indexing more than one alignment file

I'm not sure why this still fails, maybe later I'll find time to investigate.

[hexylena]

Actually not sure why this task is so complicated, it can be simplified to just

@@ -348,18 +344,11 @@ task Index {
     String bamIndexPath = sub(outputPath, "\.bam$", ".bai")
 
     command {
-        bash -c '
-        set -e
-        # Make sure outputBamPath does not exist.
-        if [ ! -f ~{outputPath} ]
-        then
-            mkdir -p "$(dirname ~{outputPath})"
-            ln ~{bamFile} ~{outputPath} || cp ~{bamFile} ~{outputPath}
-        fi
+        mkdir -p "$(dirname ~{outputPath})"
+
         samtools index \
         --threads ~{threads -1} \
-        ~{outputPath} ~{bamIndexPath}
-        '
+        ~{bamFile} ~{bamIndexPath}
     }
 
     output {

[hexylena]

guessing this task isn't used much

[DavyCats]

No, usually we just generate the index in the task that also made the BAM file. If I recall correctly, this logic was added to ensure that the BAM and the index are in the same folder to ensure they will get localized together.

It looks like there is something going wrong with the input here though. It's trying to create a link to a bam file (ILX.bam), but calling it an index (ILX.bam.bai). Samtools index is then given the same path twice. It might that this is causing the error error. I guess you gave the intended .bai path to outputBamPath, but this should be the name of the output bam.