# The output of the process is not accessible

**URL:** <https://community.seqera.io/t/the-output-of-the-process-is-not-accessible/559>\
**Category:** Ask for help\
**Created:** [March 13, 2024, 9:24am UTC](https://community.seqera.io/t/the-output-of-the-process-is-not-accessible/559 "2024-03-13T09:24:25Z")\
**Posts on this page:** 6\
**Page:** 1

<div class="post-metadata">

**Author:** ![CecCADS](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/ceccads/32/537_2.png) [@CecCADS](https://community.seqera.io/u/CecCADS)\
**Post date:** [March 13, 2024, 9:24am UTC](https://community.seqera.io/t/the-output-of-the-process-is-not-accessible/559/1 "2024-03-13T09:24:25Z")

</div>

Hi, I’m completely new to Nextflow and I would need some help please:

1. I created a docker container using the following Dockerfile :

```auto
FROM python:3.10

LABEL image.author.name "..."
LABEL image.author.email "..."

# Install required packages including Bash and ps
RUN apt-get update && \
    apt-get install -y bash procps && \
    apt-get clean

# Set Bash as the default shell
SHELL ["/bin/bash", "-c"]

# Set working directory
WORKDIR /app

# Copy the requirements.txt file into the container
COPY requirements.txt .

# Install required packages using pip
RUN pip install --no-cache-dir -r requirements.txt

# Set Bash as the container entrypoint
ENTRYPOINT ["/bin/bash", "-l", "-c"]

```

with “requirements.txt” a list of python packages.

I build my container using  
`docker build -t myimage .`

Using `docker images` I can see that it has been created, and using `docker run -i myimage "echo 'hello'"` I see that it works fine.

1. in the nextflow.config I have:

```auto
process.container = 'myimage' 
docker.enabled = true

```

1. my workflow reads as

```auto
process sayHello {
    output:
    stdout

    """
    echo Hello world!
    """
}

workflow {
    sayHello | view { "I say... $it" }
}

```

1. the output reads as `I say... ` =\> it seems that the stdout output is not accessible.

Similarly, I tried to create .csv file in the process using python code and they are not saved anywhere.

Would anyone know what I’m missing here? I’m working on macOS. As I don’t get any error messages and that I’m completely new to Nextflow, i’m a bit lost…

Thank you so much for your help!

---

<div class="post-metadata">

**Author:** ![Adam\_Talbot](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/adam_talbot/32/62_2.png) [@Adam\_Talbot](https://community.seqera.io/u/Adam_Talbot)\
**Post date:** [March 13, 2024, 9:52am UTC](https://community.seqera.io/t/the-output-of-the-process-is-not-accessible/559/2 "2024-03-13T09:52:12Z")

</div>

That works fine on my machine. One thing I would recommend is to not use ENTRTYPOINT, it’s designed for making a Docker file an executable. In general, I would avoid it unless you _really_ need it.

Try using `process.container = 'docker.io/debian:trixie-slim'` which will pull a [public container](https://hub.docker.com/layers/library/debian/trixie-slim/images/sha256-d4e306f14b8b7389b36be8fb0eadab638cb7744546a33a74f0fc27bb9037dc14?context=explore) which definitely works.

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<div class="post-metadata">

**Author:** ![CecCADS](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/ceccads/32/537_2.png) [@CecCADS](https://community.seqera.io/u/CecCADS)\
**Post date:** [March 13, 2024, 10:20am UTC](https://community.seqera.io/t/the-output-of-the-process-is-not-accessible/559/3 "2024-03-13T10:20:47Z")

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Hi @Adam_Talbot, thank you very much! you are right, if I remove the entrypoint from my dockerfile it works! However, the reason I added it is because of the [container documentation](https://www.nextflow.io/docs/latest/container.html#id5), which says " Also, Bash should be available on the path `/bin/bash` and it should be the container entrypoint." Shouldn’t I use the entrypoint in the dockerfile for this? Thanks a lot for the help!

---

<div class="post-metadata">

**Author:** ![Adam\_Talbot](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/adam_talbot/32/62_2.png) [@Adam\_Talbot](https://community.seqera.io/u/Adam_Talbot)\
**Post date:** [March 13, 2024, 10:48am UTC](https://community.seqera.io/t/the-output-of-the-process-is-not-accessible/559/4 "2024-03-13T10:48:48Z")

</div>

This really means ‘don’t set `ENTRYPOINT=python mytool.py`’. This is something a number of Docker images do to make them a container as software, but for Nextflow they just get in the way.

Nextflow will run the container with a command that is essentially `docker run containerName /bin/bash -ue ${process.script}`, so in general, you can leave ENTRYPOINT alone and Nextflow should work fine.

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<div class="post-metadata">

**Author:** ![CecCADS](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/ceccads/32/537_2.png) [@CecCADS](https://community.seqera.io/u/CecCADS)\
**Post date:** [March 13, 2024, 12:45pm UTC](https://community.seqera.io/t/the-output-of-the-process-is-not-accessible/559/5 "2024-03-13T12:45:10Z")

</div>

Thank you very much for the clarification!

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<div class="post-metadata">

**Author:** ![system](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/system/32/2402_2.png) [@system](https://community.seqera.io/u/system)\
**Post date:** [March 20, 2024, 12:45pm UTC](https://community.seqera.io/t/the-output-of-the-process-is-not-accessible/559/6 "2024-03-20T12:45:45Z")

</div>

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