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Update 05-processes-part2.md
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remove tree command fixes @HadrienG review comment 

"tree is not available on macOS by default. Personally, I'd avoid using it"
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ggrimes authored Apr 24, 2024
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26 changes: 12 additions & 14 deletions episodes/05-processes-part2.md
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Expand Up @@ -696,19 +696,17 @@ N E X T F L O W ~ version 21.04.0
Launching `process_publishDir.nf` [friendly_pauling] - revision: 9b5c315893
executor > local (1)
[d9/909ed9] process > COMBINE_READS (1) [100%] 1 of 1 ✔
[a1/5956bd] process > COMBINE_READS (1) [100%] 1 of 1 ✔
```

We can use the UNIX command `tree` to examine the contents of the results directory.
We can use the UNIX command `ls -l` to examine the contents of the results directory.

```bash
tree results
ls -l results/merged_reads/ref1.merged.fq.gz
```

```output
results/
└── merged_reads
└── ref1.merged.fq.gz -> work/48/f97234d7185cbfbd86e2f11c1afab5/ref1.merged.fq.gz
results/merged_reads/ref1.merged.fq.gz -> /Users/nf-user/nf-training/work/a1/5956bd9a92f13694b3ada1941f0d2d/ref1.merged.fq.gz
```

In the above example, the `publishDir "results/merged_reads"`, creates a symbolic link `->` to the output files specified by the process `merged_reads` to the directory path `results/merged_reads`.
Expand Down Expand Up @@ -786,18 +784,18 @@ executor > local (1)
[be/950786] process > SPLIT_FASTA (1) [100%] 1 of 1 ✔
```

We can now use the `tree` command to examine the results directory.
We can now use the `ls results/*` command to examine the results directory.

```bash
$ tree results
$ls results/*
```

```output
results/
├── sequence
│   └── sequence.txt
└── ids
└── sequence_ids.txt
```output
results/ids:
sequence_ids.txt
results/sequence:
sequence.txt
```

::::::::::::::::::::::::::::::::::::::: challenge
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